Read coverage calculator for metagenomics
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FASTA/FASTQ pre-processing programs
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base-accurate DNA sequence alignments using WFA and mashmap2
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web-based protein structure viewer and analysis tool interactively or in batch mode
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machine learning for genomic variants
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Clustering scRNAseq by genotypes
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"Unsupervised Discovery of Object Landmarks as Structural Representations" Project page: http://www.ytzhang.net/projects/lmdis-rep/
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Tools for manipulating sequence graphs in the GFA and rGFA formats
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序列号生成器－－《万亿级调用系统：微信序列号生成器架构设计及演变》开源实现
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pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
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SMC++ infers population history from whole-genome sequence data.
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Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
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Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
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diploid SNV caller for error-prone reads
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⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
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BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data
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Easily install all nanopack scripts together
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Finder of Somatic Fusion Genes in RNA-seq data
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A script for balancing predictions which helps in achieving high results on Kaggle
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GeneWalk identifies relevant gene functions for a biological context using network representation learning
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Turn Java 8 Streams into Unix like pipelines
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A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
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Gene set variation analysis
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Overlapping git repositories
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A structural variation pipeline for short-read sequencing
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A gap-closing software tool that uses long reads to enhance genome assembly.
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A minimap2 frontend for PacBio native data formats
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Scripts to analyse large Git repositories.
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An efficient FASTQ manipulation suite
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WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
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A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
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A variational framework for inferring population structure from SNP genotype data.
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Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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tools for genetic genealogy and the analysis of consumer DNA test results
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Batch balanced KNN
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Pandas utilities for tab-delimited and other genomic data files
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Large Graph Layout
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R package for the analysis of massive SNP arrays.
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A scalable genome browser. Apache 2 licensed.
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A software package for analyzing snapshots of developmental processes
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breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
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HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
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Population-scale genomics
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Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
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Integrated Differential Expression and Pathway analysis
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Benchmarking programming languages/implementations for common tasks in Bioinformatics
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Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
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CoverMby wwood
Read coverage calculator for metagenomics
Rust
125Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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fastx_toolkitby agordon
FASTA/FASTQ pre-processing programs
C 125Updated: 4 y ago License: Proprietary (Proprietary)
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wfmashby waveygang
base-accurate DNA sequence alignments using WFA and mashmap2
C++ 125Updated: 2 y ago License: Permissive (MIT)
125Updated: 2 y ago License: Permissive (MIT)Support
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icn3dby ncbi
web-based protein structure viewer and analysis tool interactively or in batch mode
JavaScript 124Updated: 2 y ago License: Proprietary (Proprietary)
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VariantSparkby aehrc
machine learning for genomic variants
JavaScript 124Updated: 2 y ago License: Proprietary (Proprietary)
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souporcellby wheaton5
Clustering scRNAseq by genotypes
Python 123Updated: 2 y ago License: Permissive (MIT)
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lmdis-repby YutingZhang
"Unsupervised Discovery of Object Landmarks as Structural Representations" Project page: http://www.ytzhang.net/projects/lmdis-rep/
Python 123Updated: 4 y ago License: Permissive (Apache-2.0)
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gfatoolsby lh3
Tools for manipulating sequence graphs in the GFA and rGFA formats
C 123Updated: 3 y ago
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seqsvrby teamgram
序列号生成器－－《万亿级调用系统：微信序列号生成器架构设计及演变》开源实现
Go 123Updated: 3 y ago License: Permissive (Apache-2.0)
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pycoQCby tleonardi
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
Python 122Updated: 4 y ago License: Strong Copyleft (GPL-3.0)
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smcppby popgenmethods
SMC++ infers population history from whole-genome sequence data.
C++ 122Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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FREECby BoevaLab
Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
C++ 122Updated: 2 y ago License: No License (No License)
122Updated: 2 y ago License: No License (No License)Support
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trimalby inab
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
C++ 122Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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seq2scienceby vanheeringen-lab
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
Python 121Updated: 2 y ago License: Permissive (MIT)
121Updated: 2 y ago License: Permissive (MIT)Support
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longshotby pjedge
diploid SNV caller for error-prone reads
Rust 121Updated: 2 y ago License: Permissive (MIT)
121Updated: 2 y ago License: Permissive (MIT)Support
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shovillby tseemann
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
Perl 121Updated: 4 y ago License: Strong Copyleft (GPL-3.0)
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BIGSIby Phelimb
BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data
Python 120Updated: 3 y ago License: Permissive (MIT)
120Updated: 3 y ago License: Permissive (MIT)Support
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nanopackby wdecoster
Easily install all nanopack scripts together
Python 120Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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fusioncatcherby ndaniel
Finder of Somatic Fusion Genes in RNA-seq data
Python 120Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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predictions_balancingby PavelOstyakov
A script for balancing predictions which helps in achieving high results on Kaggle
Python 119Updated: 4 y ago License: Permissive (MIT)
119Updated: 4 y ago License: Permissive (MIT)Support
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genewalkby churchmanlab
GeneWalk identifies relevant gene functions for a biological context using network representation learning
Python 119Updated: 2 y ago License: Permissive (BSD-2-Clause)
119Updated: 2 y ago License: Permissive (BSD-2-Clause)Support
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unix-streamby benas
Turn Java 8 Streams into Unix like pipelines
Java 119Updated: 4 y ago License: Permissive (MIT)
119Updated: 4 y ago License: Permissive (MIT)Support
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genozipby divonlan
A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
C 119Updated: 2 y ago License: Proprietary (Proprietary)
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gatk-svby broadinstitute
A structural variation pipeline for short-read sequencing
Python 119Updated: 2 y ago License: Permissive (BSD-3-Clause)
119Updated: 2 y ago License: Permissive (BSD-3-Clause)Support
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CeTuneby intel
Python 118Updated: 4 y ago License: Proprietary (Proprietary)
118Updated: 4 y ago License: Proprietary (Proprietary)Support
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TGS-GapCloserby BGI-Qingdao
A gap-closing software tool that uses long reads to enhance genome assembly.
C++ 118Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
118Updated: 2 y ago License: Strong Copyleft (GPL-3.0)Support
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pbmm2by PacificBiosciences
A minimap2 frontend for PacBio native data formats
Perl 118Updated: 2 y ago License: Permissive (BSD-3-Clause-Clear)
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git-repo-analysisby larsxschneider
Scripts to analyse large Git repositories.
Shell 118Updated: 4 y ago License: Permissive (MIT)
118Updated: 4 y ago License: Permissive (MIT)Support
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fqtoolsby alastair-droop
An efficient FASTQ manipulation suite
C 118Updated: 4 y ago License: Strong Copyleft (GPL-3.0)
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methylpyby yupenghe
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
Python 117Updated: 2 y ago License: Permissive (Apache-2.0)
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kb_pythonby pachterlab
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
Python 117Updated: 2 y ago License: Permissive (BSD-2-Clause)
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fastStructureby rajanil
A variational framework for inferring population structure from SNP genotype data.
Python 117Updated: 2 y ago License: Permissive (MIT)
117Updated: 2 y ago License: Permissive (MIT)Support
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CRISPRessoby lucapinello
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
Python 117Updated: 4 y ago License: Strong Copyleft (AGPL-3.0)
117Updated: 4 y ago License: Strong Copyleft (AGPL-3.0)Support
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lineageby apriha
tools for genetic genealogy and the analysis of consumer DNA test results
Python 117Updated: 2 y ago License: Permissive (MIT)
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bioframeby open2c
Pandas utilities for tab-delimited and other genomic data files
Python 117Updated: 2 y ago License: Permissive (MIT)
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bigsnprby privefl
R package for the analysis of massive SNP arrays.
R 117Updated: 3 y ago License: No License (No License)
117Updated: 3 y ago License: No License (No License)Support
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mangoby bigdatagenomics
A scalable genome browser. Apache 2 licensed.
Scala 117Updated: 2 y ago License: Permissive (Apache-2.0)
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wotby broadinstitute
A software package for analyzing snapshots of developmental processes
Jupyter Notebook 117Updated: 2 y ago License: Permissive (BSD-3-Clause)
117Updated: 2 y ago License: Permissive (BSD-3-Clause)Support
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breseqby barricklab
breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
C++ 117Updated: 2 y ago License: Strong Copyleft (GPL-2.0)
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humannby biobakery
HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
Python 116Updated: 2 y ago License: Proprietary (Proprietary)
116Updated: 2 y ago License: Proprietary (Proprietary)Support
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rna-seq-pipelineby ENCODE-DCC
Python 116Updated: 2 y ago License: Permissive (MIT)
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celdaby campbio
Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
R 116Updated: 2 y ago License: Permissive (MIT)
116Updated: 2 y ago License: Permissive (MIT)Support
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idepby iDEP-SDSU
Integrated Differential Expression and Pathway analysis
R 116Updated: 2 y ago License: No License (No License)
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biofastby lh3
Benchmarking programming languages/implementations for common tasks in Bioinformatics
C 116Updated: 4 y ago License: No License (No License)
116Updated: 4 y ago License: No License (No License)Support
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ARMORby csoneson
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
R 116Updated: 4 y ago License: Permissive (MIT)
116Updated: 4 y ago License: Permissive (MIT)Support
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