Genomics Libraries - Page 1

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biopythonby biopython

Python dotstar image 3633 dotVersion:Currentdot
License: Proprietary (Proprietary)

Official git repository for Biopython (originally converted from CVS)

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            HTML dotstar image 3499 dotVersion:Currentdot
            License: Proprietary (Proprietary)

            Data Science at the Command Line

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                      pandarallelby nalepae

                      Python dotstar image 3108 dotVersion:Currentdot
                      License: Permissive (BSD-3-Clause)

                      A simple and efficient tool to parallelize Pandas operations on all available CPUs

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                                deepvariantby google

                                Python dotstar image 2819 dotVersion:Currentdot
                                License: Permissive (BSD-3-Clause)

                                DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

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                                          seuratby satijalab

                                          R dotstar image 1834 dotVersion:Currentdot
                                          License: Proprietary (Proprietary)

                                          R toolkit for single cell genomics

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                                                    OpenWormby openworm

                                                    Python dotstar image 1762 dotVersion:Currentdot
                                                    License: Permissive (MIT)

                                                    Repository for the main Dockerfile with the Openworm software stack and project-wide issues

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                                                              fastpby OpenGene

                                                              C++ dotstar image 1525 dotVersion:Currentdot
                                                              License: Permissive (MIT)

                                                              An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

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                                                                        STARby alexdobin

                                                                        C dotstar image 1508 dotVersion:Currentdot
                                                                        License: Permissive (MIT)

                                                                        RNA-seq aligner

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                                                                                  scanpyby scverse

                                                                                  Python dotstar image 1497 dotVersion:Currentdot
                                                                                  License: Permissive (BSD-3-Clause)

                                                                                  Single-cell analysis in Python. Scales to >1M cells.

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                                                                                            bioconda-recipesby bioconda

                                                                                            Shell dotstar image 1491 dotVersion:Currentdot
                                                                                            License: Permissive (MIT)

                                                                                            Conda recipes for the bioconda channel.

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                                                                                                      minimap2by lh3

                                                                                                      C dotstar image 1468 dotVersion:Currentdot
                                                                                                      License: Proprietary (Proprietary)

                                                                                                      A versatile pairwise aligner for genomic and spliced nucleotide sequences

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                                                                                                                gatkby broadinstitute

                                                                                                                Java dotstar image 1450 dotVersion:Currentdot
                                                                                                                License: Proprietary (Proprietary)

                                                                                                                Official code repository for GATK versions 4 and up

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                                                                                                                          samtoolsby samtools

                                                                                                                          C dotstar image 1358 dotVersion:Currentdot
                                                                                                                          License: Proprietary (Proprietary)

                                                                                                                          Tools (written in C using htslib) for manipulating next-generation sequencing data

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                                                                                                                                    bwaby lh3

                                                                                                                                    C dotstar image 1308 dotVersion:Currentdot
                                                                                                                                    License: Strong Copyleft (GPL-3.0)

                                                                                                                                    Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

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                                                                                                                                              gentleby lowerquality

                                                                                                                                              Python dotstar image 1263 dotVersion:Currentdot
                                                                                                                                              License: Permissive (MIT)

                                                                                                                                              gentle forced aligner

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                                                                                                                                                        rnaseq_tutorialby griffithlab

                                                                                                                                                        R dotstar image 1248 dotVersion:Currentdot
                                                                                                                                                        License: Proprietary (Proprietary)

                                                                                                                                                        Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

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                                                                                                                                                                  seqtkby lh3

                                                                                                                                                                  C dotstar image 1154 dotVersion:Currentdot
                                                                                                                                                                  License: Permissive (MIT)

                                                                                                                                                                  Toolkit for processing sequences in FASTA/Q formats

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                                                                                                                                                                            galaxyby galaxyproject

                                                                                                                                                                            Python dotstar image 1116 dotVersion:Currentdot
                                                                                                                                                                            License: Proprietary (Proprietary)

                                                                                                                                                                            Data intensive science for everyone.

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                                                                                                                                                                                      Jupyter Notebook dotstar image 1076 dotVersion:Currentdot
                                                                                                                                                                                      no licences License: No License (No License)

                                                                                                                                                                                      Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

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                                                                                                                                                                                                seqkitby shenwei356

                                                                                                                                                                                                Go dotstar image 1026 dotVersion:Currentdot
                                                                                                                                                                                                License: Permissive (MIT)

                                                                                                                                                                                                A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

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                                                                                                                                                                                                          MultiQCby ewels

                                                                                                                                                                                                          Python dotstar image 1019 dotVersion:Currentdot
                                                                                                                                                                                                          License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                                          Aggregate results from bioinformatics analyses across many samples into a single report.

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                                                                                                                                                                                                                    MMseqs2by soedinglab

                                                                                                                                                                                                                    C dotstar image 970 dotVersion:Currentdot
                                                                                                                                                                                                                    License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                                                    MMseqs2: ultra fast and sensitive search and clustering suite

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                                                                                                                                                                                                                              scvi-toolsby scverse

                                                                                                                                                                                                                              Python dotstar image 937 dotVersion:Currentdot
                                                                                                                                                                                                                              License: Permissive (BSD-3-Clause)

                                                                                                                                                                                                                              Deep probabilistic analysis of single-cell omics data

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                                                                                                                                                                                                                                        vgby vgteam

                                                                                                                                                                                                                                        C++ dotstar image 931 dotVersion:Currentdot
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                                                                                                                                                                                                                                        tools for working with genome variation graphs

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                                                                                                                                                                                                                                                  Python dotstar image 923 dotVersion:Currentdot
                                                                                                                                                                                                                                                  License: Permissive (MIT)

                                                                                                                                                                                                                                                  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

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                                                                                                                                                                                                                                                            sra-toolsby ncbi

                                                                                                                                                                                                                                                            C dotstar image 918 dotVersion:Currentdot
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                                                                                                                                                                                                                                                            SRA Tools

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                                                                                                                                                                                                                                                                      hailby hail-is

                                                                                                                                                                                                                                                                      Python dotstar image 881 dotVersion:Currentdot
                                                                                                                                                                                                                                                                      License: Permissive (MIT)

                                                                                                                                                                                                                                                                      Cloud-native genomic dataframes and batch computing

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                                                                                                                                                                                                                                                                                Shell dotstar image 878 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                no licences License: No License (No License)

                                                                                                                                                                                                                                                                                Unix, R and python tools for genomics and data science

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                                                                                                                                                                                                                                                                                          picardby broadinstitute

                                                                                                                                                                                                                                                                                          Java dotstar image 873 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                          License: Permissive (MIT)

                                                                                                                                                                                                                                                                                          A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

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                                                                                                                                                                                                                                                                                                    bedtools2by arq5x

                                                                                                                                                                                                                                                                                                    C dotstar image 825 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                    License: Permissive (MIT)

                                                                                                                                                                                                                                                                                                    bedtools - the swiss army knife for genome arithmetic

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                                                                                                                                                                                                                                                                                                              diamondby bbuchfink

                                                                                                                                                                                                                                                                                                              C++ dotstar image 821 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                              License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                                                                                                                                              Accelerated BLAST compatible local sequence aligner.

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                                                                                                                                                                                                                                                                                                                        clusterProfilerby YuLab-SMU

                                                                                                                                                                                                                                                                                                                        R dotstar image 779 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                        no licences License: No License (No License)

                                                                                                                                                                                                                                                                                                                        :bar_chart: A universal enrichment tool for interpreting omics data

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                                                                                                                                                                                                                                                                                                                                  f

                                                                                                                                                                                                                                                                                                                                  Python dotstar image 767 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                  License: Proprietary (Proprietary)

                                                                                                                                                                                                                                                                                                                                  A collection of links and notes on forced alignment tools

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                                                                                                                                                                                                                                                                                                                                            n

                                                                                                                                                                                                                                                                                                                                            Python dotstar image 759 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                            License: Permissive (Apache-2.0)

                                                                                                                                                                                                                                                                                                                                            Scripts to download genomes from the NCBI FTP servers

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                                                                                                                                                                                                                                                                                                                                                      RNA-seq-analysisby crazyhottommy

                                                                                                                                                                                                                                                                                                                                                      Python dotstar image 757 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                      License: Permissive (MIT)

                                                                                                                                                                                                                                                                                                                                                      RNAseq analysis notes from Ming Tang

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                                                                                                                                                                                                                                                                                                                                                                ggetby pachterlab

                                                                                                                                                                                                                                                                                                                                                                Python dotstar image 751 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                License: Permissive (BSD-2-Clause)

                                                                                                                                                                                                                                                                                                                                                                🧬 gget enables efficient querying of genomic reference databases

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                                                                                                                                                                                                                                                                                                                                                                          trinityrnaseqby trinityrnaseq

                                                                                                                                                                                                                                                                                                                                                                          Perl dotstar image 735 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                          License: Permissive (BSD-3-Clause)

                                                                                                                                                                                                                                                                                                                                                                          Trinity RNA-Seq de novo transcriptome assembly

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                                                                                                                                                                                                                                                                                                                                                                                    nucleusby google

                                                                                                                                                                                                                                                                                                                                                                                    C++ dotstar image 734 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                    License: Proprietary (Proprietary)

                                                                                                                                                                                                                                                                                                                                                                                    Python and C++ code for reading and writing genomics data.

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                                                                                                                                                                                                                                                                                                                                                                                              C++ dotstar image 719 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                              License: Permissive (CC0-1.0)

                                                                                                                                                                                                                                                                                                                                                                                              A scalable pipeline for designing reconfigurable organisms

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                                                                                                                                                                                                                                                                                                                                                                                                        ikvmby ikvm-revived

                                                                                                                                                                                                                                                                                                                                                                                                        C# dotstar image 717 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                        License: Proprietary (Proprietary)

                                                                                                                                                                                                                                                                                                                                                                                                        A Java Virtual Machine and Bytecode-to-IL Converter for .NET

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                                                                                                                                                                                                                                                                                                                                                                                                                  htslibby samtools

                                                                                                                                                                                                                                                                                                                                                                                                                  C dotstar image 696 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                  License: Proprietary (Proprietary)

                                                                                                                                                                                                                                                                                                                                                                                                                  C library for high-throughput sequencing data formats

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                                                                                                                                                                                                                                                                                                                                                                                                                            eteby etetoolkit

                                                                                                                                                                                                                                                                                                                                                                                                                            Python dotstar image 694 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                            License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                                                                                                                                                                                                                                                            Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

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                                                                                                                                                                                                                                                                                                                                                                                                                                      freebayesby freebayes

                                                                                                                                                                                                                                                                                                                                                                                                                                      C++ dotstar image 685 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                                      License: Permissive (MIT)

                                                                                                                                                                                                                                                                                                                                                                                                                                      Bayesian haplotype-based genetic polymorphism discovery and genotyping.

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                                                                                                                                                                                                                                                                                                                                                                                                                                                TBtoolsby CJ-Chen

                                                                                                                                                                                                                                                                                                                                                                                                                                                Shell dotstar image 683 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                                                no licences License: No License (No License)

                                                                                                                                                                                                                                                                                                                                                                                                                                                GUI/CommandLine Tool Box for biologistists to utilize NGS data.

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                                                                                                                                                                                                                                                                                                                                                                                                                                                          seqby seq-lang

                                                                                                                                                                                                                                                                                                                                                                                                                                                          C++ dotstar image 678 dotVersion:Currentdot
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                                                                                                                                                                                                                                                                                                                                                                                                                                                          A high-performance, Pythonic language for bioinformatics

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                    sentence2vecby klb3713

                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Python dotstar image 671 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    no licences License: No License (No License)

                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Tools for mapping a sentence with arbitrary length to vector space

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                              prokkaby tseemann

                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Perl dotstar image 666 dotVersion:Currentdot
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                              :zap: :aquarius: Rapid prokaryotic genome annotation

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        scvi-toolsby YosefLab

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Python dotstar image 659 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        License: Permissive (BSD-3-Clause)

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Deep probabilistic analysis of single-cell omics data

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  pysamby pysam-developers

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  License: Permissive (MIT)

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            khmerby dib-lab

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            License: Proprietary (Proprietary)

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      biopythonby biopython
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Official git repository for Biopython (originally converted from CVS)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                data-science-at-the-command-lineby jeroenjanssens
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Data Science at the Command Line
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          pandarallelby nalepae
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          A simple and efficient tool to parallelize Pandas operations on all available CPUs
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    deepvariantby google
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              seuratby satijalab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              R toolkit for single cell genomics
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        OpenWormby openworm
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Repository for the main Dockerfile with the Openworm software stack and project-wide issues
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  fastpby OpenGene
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            STARby alexdobin
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            RNA-seq aligner
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      scanpyby scverse
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Single-cell analysis in Python. Scales to >1M cells.
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                bioconda-recipesby bioconda
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Conda recipes for the bioconda channel.
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          minimap2by lh3
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          A versatile pairwise aligner for genomic and spliced nucleotide sequences
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    gatkby broadinstitute
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Official code repository for GATK versions 4 and up
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              samtoolsby samtools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Tools (written in C using htslib) for manipulating next-generation sequencing data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Cdotstar image 1358dotUpdated: 1 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        bwaby lh3
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Cdotstar image 1308dotUpdated: 1 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  gentleby lowerquality
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  gentle forced aligner
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            rnaseq_tutorialby griffithlab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Rdotstar image 1248dotUpdated: 1 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      seqtkby lh3
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Toolkit for processing sequences in FASTA/Q formats
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Cdotstar image 1154dotUpdated: 1 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                galaxyby galaxyproject
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Data intensive science for everyone.
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          single-cell-tutorialby theislab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Jupyter Notebookdotstar image 1076dotUpdated: 1 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    seqkitby shenwei356
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              MultiQCby ewels
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Aggregate results from bioinformatics analyses across many samples into a single report.
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        MMseqs2by soedinglab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        MMseqs2: ultra fast and sensitive search and clustering suite
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  scvi-toolsby scverse
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Deep probabilistic analysis of single-cell omics data
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            vgby vgteam
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            tools for working with genome variation graphs
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      bcbio-nextgenby bcbio
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Pythondotstar image 923dotUpdated: 1 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                sra-toolsby ncbi
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SRA Tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Cdotstar image 918dotUpdated: 1 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          hailby hail-is
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Cloud-native genomic dataframes and batch computing
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Pythondotstar image 881dotUpdated: 1 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    getting-started-with-genomics-tools-and-resourcesby crazyhottommy
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Unix, R and python tools for genomics and data science
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Shelldotstar image 878dotUpdated: 1 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              picardby broadinstitute
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Javadotstar image 873dotUpdated: 1 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        bedtools2by arq5x
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        bedtools - the swiss army knife for genome arithmetic
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  diamondby bbuchfink
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Accelerated BLAST compatible local sequence aligner.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  C++dotstar image 821dotUpdated: 1 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            clusterProfilerby YuLab-SMU
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            :bar_chart: A universal enrichment tool for interpreting omics data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Rdotstar image 779dotUpdated: 1 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      forced-alignment-toolsby pettarin
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      A collection of links and notes on forced alignment tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Pythondotstar image 767dotUpdated: 1 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ncbi-genome-downloadby kblin
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Scripts to download genomes from the NCBI FTP servers
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Pythondotstar image 759dotUpdated: 1 y agodot License: Permissive (Apache-2.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          RNA-seq-analysisby crazyhottommy
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          RNAseq analysis notes from Ming Tang
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Pythondotstar image 757dotUpdated: 1 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ggetby pachterlab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    🧬 gget enables efficient querying of genomic reference databases
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pythondotstar image 751dotUpdated: 1 y agodot License: Permissive (BSD-2-Clause)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              trinityrnaseqby trinityrnaseq
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Trinity RNA-Seq de novo transcriptome assembly
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Perldotstar image 735dotUpdated: 1 y agodot License: Permissive (BSD-3-Clause)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        nucleusby google
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Python and C++ code for reading and writing genomics data.
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  reconfigurable_organismsby skriegman
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  A scalable pipeline for designing reconfigurable organisms
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  C++dotstar image 719dotUpdated: 3 y agodot License: Permissive (CC0-1.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ikvmby ikvm-revived
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            A Java Virtual Machine and Bytecode-to-IL Converter for .NET
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            C#dotstar image 717dotUpdated: 1 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      htslibby samtools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      C library for high-throughput sequencing data formats
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Cdotstar image 696dotUpdated: 1 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                eteby etetoolkit
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Pythondotstar image 694dotUpdated: 1 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          freebayesby freebayes
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Bayesian haplotype-based genetic polymorphism discovery and genotyping.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          C++dotstar image 685dotUpdated: 1 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    TBtoolsby CJ-Chen
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    GUI/CommandLine Tool Box for biologistists to utilize NGS data.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Shelldotstar image 683dotUpdated: 1 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              seqby seq-lang
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              A high-performance, Pythonic language for bioinformatics
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        sentence2vecby klb3713
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Tools for mapping a sentence with arbitrary length to vector space
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  prokkaby tseemann
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  :zap: :aquarius: Rapid prokaryotic genome annotation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Perldotstar image 666dotUpdated: 1 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            scvi-toolsby YosefLab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Deep probabilistic analysis of single-cell omics data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Pythondotstar image 659dotUpdated: 2 y agodot License: Permissive (BSD-3-Clause)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      pysamby pysam-developers
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                khmerby dib-lab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Pythondotstar image 647dotUpdated: 3 y agodot License: Proprietary (Proprietary)
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