Genomics Libraries - Page 5

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

Perl 270Updated: 1 y ago License: Strong Copyleft (GPL-2.0)

Tools for working with genomic and high throughput sequencing data.

Scala 269Updated: 2 y ago License: Permissive (MIT)

:microscope: Assemble large genomes using short reads

C++ 268Updated: 2 y ago License: Proprietary (Proprietary)

Analyze documents with Amazon Textract and generate output in multiple formats.

Jupyter Notebook 267Updated: 2 y ago License: Permissive (Apache-2.0)

cython + htslib == fast VCF and BCF processing

Python 266Updated: 3 y ago License: Permissive (MIT)

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

C++ 266Updated: 2 y ago License: Permissive (Apache-2.0)

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

Kotlin 264Updated: 1 y ago License: Proprietary (Proprietary)

Table of software for the analysis of single-cell RNA-seq data.

R 264Updated: 2 y ago License: Permissive (MIT)

annotate a VCF with other VCFs/BEDs/tabixed files

Go 263Updated: 4 y ago License: Permissive (MIT)

Reference mapping for single-cell genomics

Jupyter Notebook 263Updated: 2 y ago License: Permissive (BSD-3-Clause)

A Java API for high-throughput sequencing data (HTS) formats.

Java 260Updated: 2 y ago License: No License (No License)

Formalizing and benchmarking open problems in single-cell genomics

Jupyter Notebook 260Updated: 1 y ago License: Permissive (MIT)

RNA-seq workflow using STAR and DESeq2

Python 258Updated: 2 y ago License: Permissive (MIT)

Test-Driven Data Analysis Functions

Python 257Updated: 2 y ago License: Permissive (MIT)

A complete pipeline for metagenomic analysis

C 257Updated: 1 y ago License: Strong Copyleft (GPL-3.0)

Core BioPerl 1.x code

Perl 256Updated: 3 y ago License: No License (No License)

Rapid large-scale prokaryote pan genome analysis

Perl 255Updated: 2 y ago License: Proprietary (Proprietary)

Welcome to the User Friendly Python Kriging Toolbox!

Python 254Updated: 3 y ago License: Permissive (MIT)

Package for fetching metadata and downloading data from SRA/ENA/GEO

Python 253Updated: 2 y ago License: Permissive (BSD-3-Clause)

Examples of single-cell genomic analysis accelerated with RAPIDS

Jupyter Notebook 252Updated: 2 y ago License: Permissive (Apache-2.0)

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

JavaScript 251Updated: 2 y ago License: Proprietary (Proprietary)

Chromosome visualization for the web

JavaScript 251Updated: 2 y ago License: Proprietary (Proprietary)

By study this, it won't be costly or time-consuming to customize a NGS data analysis pipeline

Shell 251Updated: 4 y ago License: Strong Copyleft (GPL-3.0)

microbiome R package

R 250Updated: 2 y ago License: Proprietary (Proprietary)

GenomeTools genome analysis system.

C 250Updated: 1 y ago License: Proprietary (Proprietary)

Graph-linked unified embedding for single-cell multi-omics data integration

Python 249Updated: 1 y ago License: Permissive (MIT)

Access to Biological Web Services from Python.

Python 248Updated: 2 y ago License: Proprietary (Proprietary)

De novo assembly from Oxford Nanopore reads.

C++ 248Updated: 3 y ago License: Proprietary (Proprietary)

Quickly search, compare, and analyze genomic and metagenomic data sets.

Python 247Updated: 3 y ago License: Proprietary (Proprietary)

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Python 246Updated: 2 y ago License: Proprietary (Proprietary)

Eukaryotic Genome Annotation Pipeline

Python 245Updated: 1 y ago License: Permissive (BSD-2-Clause)

A package to help convert different single-cell data formats to each other

R 244Updated: 1 y ago License: Strong Copyleft (GPL-3.0)

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

Python 243Updated: 3 y ago License: Proprietary (Proprietary)

Tabbed views for Sphinx

HTML 243Updated: 2 y ago License: Permissive (MIT)

R 241Updated: 2 y ago License: Proprietary (Proprietary)

RTG Tools: Utilities for accurate VCF comparison and manipulation

Java 239Updated: 2 y ago License: Permissive (BSD-2-Clause)

CellRank for directed single-cell fate mapping

Python 239Updated: 1 y ago License: Permissive (BSD-3-Clause)

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

Perl 239Updated: 1 y ago License: Proprietary (Proprietary)

HMMER: biological sequence analysis using profile HMMs

C 238Updated: 1 y ago License: Proprietary (Proprietary)

Extensive de-novo TE Annotator

Perl 236Updated: 2 y ago License: Strong Copyleft (GPL-3.0)

:microscope: BEDOPS: high-performance genomic feature operations

C 236Updated: 3 y ago License: Strong Copyleft (GPL-2.0)

A library of high-quality primitives that help you build accessible user interfaces with SolidJS.

TypeScript 236Updated: 2 y ago License: Proprietary (Proprietary)

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

R 235Updated: 2 y ago License: Strong Copyleft (GPL-3.0)

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

C++ 235Updated: 2 y ago License: Permissive (MIT)

Code and examples for JHU Computational Genomics class

Jupyter Notebook 235Updated: 3 y ago License: Strong Copyleft (GPL-2.0)

Pilon is an automated genome assembly improvement and variant detection tool

Scala 234Updated: 3 y ago License: Proprietary (Proprietary)

A Practical and Efficient NCBI Taxonomy Toolkit

Go 233Updated: 2 y ago License: Permissive (MIT)

elPrep: a high-performance tool for analyzing sequence alignment/map files in sequencing pipelines.

Go 233Updated: 3 y ago License: Proprietary (Proprietary)

Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

C++ 232Updated: 3 y ago License: Strong Copyleft (GPL-3.0)

A tool for generating consensus long-read assemblies for bacterial genomes

Python 231Updated: 2 y ago License: Strong Copyleft (GPL-3.0)