The Top 115 Genomics Open Source Projects

Awesome Open Source

Awesome Open Source

Combined Topics

Advertising 📦 10

Application Programming Interfaces 📦 124

Applications 📦 192

Artificial Intelligence 📦 78

Blockchain 📦 73

Build Tools 📦 113

Cloud Computing 📦 80

Code Quality 📦 28

Collaboration 📦 32

Command Line Interface 📦 49

Community 📦 83

Companies 📦 60

Compilers 📦 63

Computer Science 📦 80

Configuration Management 📦 42

Content Management 📦 175

Control Flow 📦 213

Data Formats 📦 78

Data Processing 📦 276

Data Storage 📦 135

Economics 📦 64

Frameworks 📦 215

Graphics 📦 110

Hardware 📦 152

Integrated Development Environments 📦 49

Learning Resources 📦 166

Libraries 📦 129

Lists Of Projects 📦 22

Machine Learning 📦 347

Mapping 📦 64

Marketing 📦 15

Mathematics 📦 55

Messaging 📦 98

Networking 📦 315

Operating Systems 📦 89

Operations 📦 121

Package Managers 📦 55

Programming Languages 📦 245

Runtime Environments 📦 100

Science 📦 42

Security 📦 396

Social Media 📦 27

Software Architecture 📦 72

Software Development 📦 72

Software Performance 📦 58

Software Quality 📦 133

Text Editors 📦 49

Text Processing 📦 136

User Interface 📦 330

User Interface Components 📦 514

Version Control 📦 30

Virtualization 📦 71

Web Browsers 📦 42

Web Servers 📦 26

Web User Interface 📦 210

The Top 115 Genomics Open Source Projects

Categories > Science > Genomics

Biopython ⭐ 2,693

Official git repository for Biopython (originally converted from CVS)

Deepvariant ⭐ 2,257

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

Deep Review ⭐ 1,152

A collaboratively written review paper on deep learning, genomics, and precision medicine

Official code repository for GATK versions 4 and up

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

Minimap2 ⭐ 953

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Data intensive science for everyone.

tools for working with genome variation graphs

Scalable genomic data analysis.

Nucleus ⭐ 664

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

Ncbi Genome Download ⭐ 520

Scripts to download genomes from the NCBI FTP servers

Deeptools ⭐ 458

Tools to process and analyze deep sequencing data.

Biojava ⭐ 443

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Bwa Mem2 ⭐ 427

The next version of bwa-mem

Goatools ⭐ 426

Python library to handle Gene Ontology (GO) terms

C++ library and cmdline tools for parsing and manipulating VCF files

Python library to facilitate genome assembly, annotation, and comparative genomics

Jbrowse ⭐ 396

A modern genome browser built with JavaScript and HTML5.

Bowtie2 ⭐ 373

A fast and sensitive gapped read aligner

Megahit ⭐ 348

Ultra-fast and memory-efficient (meta-)genome assembler

Gwa_tutorial ⭐ 326

A comprehensive tutorial about GWAS and PRS

Jvarkit ⭐ 319

Java utilities for Bioinformatics

Pyfaidx ⭐ 310

Efficient pythonic random access to fasta subsequences

A high-performance, Pythonic language for bioinformatics

Postgui ⭐ 280

A React web application to query and share any PostgreSQL database.

Arvados ⭐ 277

An open source platform for managing and analyzing biomedical big data

Eggnog Mapper ⭐ 265

Fast genome-wide functional annotation through orthology assignment

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Vcfanno ⭐ 262

annotate a VCF with other VCFs/BEDs/tabixed files

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Haplotype VCF comparison tools

cython + htslib == fast VCF and BCF processing

Canvasxpress ⭐ 247

JavaScript VisualizationTools

Pyranges ⭐ 235

Performant Pythonic GenomicRanges

Dragonn ⭐ 228

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

An ultrafast memory-efficient short read aligner

🔬 BEDOPS: high-performance genomic feature operations

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

Miniasm ⭐ 219

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Genomeworks ⭐ 219

SDK for GPU accelerated genome assembly and analysis

Minigraph ⭐ 217

Proof-of-concept seq-to-graph mapper and graph generator

Higlass ⭐ 213

Fast large scale matrix visualization for the web.

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Flowcraft ⭐ 209

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

Sequenceserver ⭐ 203

Intuitive local web frontend for the BLAST bioinformatics tool

Octopus ⭐ 201

Bayesian haplotype-based mutation calling

Intermine ⭐ 197

A powerful open source data warehouse system

Deep learning infrastructure for bioinformatics

Genometools ⭐ 192

GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

Ideogram ⭐ 187

Chromosome visualization for the web

Deep Rules ⭐ 184

Ten Quick Tips for Deep Learning in Biology

Rapid large-scale prokaryote pan genome analysis

Reads simulator

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

An open-source toolkit for large-scale genomic analysis

Viral Ngs ⭐ 155

Viral genomics analysis pipelines

Tools to work with variant call format files

structural variant calling and genotyping with existing tools, but, smoothly.

Hifiasm ⭐ 151

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Awesome Bioinformatics Benchmarks ⭐ 151

A curated list of bioinformatics bench-marking papers and resources.

Biomartr ⭐ 149

Genomic Data Retrieval with R

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Artemis ⭐ 139

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Snp Sites ⭐ 139

Finds SNP sites from a multi-FASTA alignment file

Miso Lims ⭐ 136

MISO: An open-source LIMS for NGS sequencing centres

Somalier ⭐ 136

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Hts Nim ⭐ 135

nim wrapper for htslib for parsing genomics data files

Benchmarking Tools ⭐ 132

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

Circlator ⭐ 131

A tool to circularize genome assemblies

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Kmer Cnt ⭐ 124

Code examples of fast and simple k-mer counters for tutorial purposes

Hicexplorer ⭐ 119

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

A cool place to store your Hi-C

NGLess: NGS with less work

An R package for creating Q-Q and manhattan plots from GWAS results

Cgranges ⭐ 113

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

variant expressions, annotation, and filtering for great good.

Msprime ⭐ 110

Simulate genealogical trees and genomic sequence data using population genetic models

Genomics ⭐ 105

A collection of scripts and notes related to genomics and bioinformatics

Smudgeplot ⭐ 104

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Gcp For Bioinformatics ⭐ 98

GCP Essentials for Bioinformatics Researchers

Antimicrobial Resistance Identification By Assembly

Chipseq_pipeline ⭐ 96

AQUAS TF and histone ChIP-seq pipeline

Genomicsqlite ⭐ 94

Genomics Extension for SQLite

Ga4gh Server ⭐ 93

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

Bioinformatics library for .NET

Pan-genome wide association studies

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features

Igv Snapshot Automator ⭐ 87

Script to automatically create and run IGV snapshot batchscripts

Awesome 10x Genomics ⭐ 82

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Sibeliaz ⭐ 80

A fast whole-genome aligner based on de Bruijn graphs

Bayesian genotyper for structural variants

Fastq.bio ⭐ 75

An interactive web tool for quality control of DNA sequencing data

Flexible genotype query among 30,000+ samples whole-genome

Assembly Stats ⭐ 70

Get assembly statistics from FASTA and FASTQ files

Bluegenes ⭐ 70

A friendly next-generation interface for Genomic data discovery powered by InterMine

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

A Go package for engineering organisms.

1-100 of 115 projects

Advertising 📦 10

Application Programming Interfaces 📦 124

Applications 📦 192

Artificial Intelligence 📦 78

Blockchain 📦 73

Build Tools 📦 113

Cloud Computing 📦 80

Code Quality 📦 28

Collaboration 📦 32

Command Line Interface 📦 49

Community 📦 83

Companies 📦 60

Compilers 📦 63

Computer Science 📦 80

Configuration Management 📦 42

Content Management 📦 175

Control Flow 📦 213

Data Formats 📦 78

Data Processing 📦 276

Data Storage 📦 135

Economics 📦 64

Frameworks 📦 215

Graphics 📦 110

Hardware 📦 152

Integrated Development Environments 📦 49

Learning Resources 📦 166

Libraries 📦 129

Lists Of Projects 📦 22

Machine Learning 📦 347

Mapping 📦 64

Marketing 📦 15

Mathematics 📦 55

Messaging 📦 98

Networking 📦 315

Operating Systems 📦 89

Operations 📦 121

Package Managers 📦 55

Programming Languages 📦 245

Runtime Environments 📦 100

Science 📦 42

Security 📦 396

Social Media 📦 27

Software Architecture 📦 72

Software Development 📦 72

Software Performance 📦 58

Software Quality 📦 133

Text Editors 📦 49

Text Processing 📦 136

User Interface 📦 330

User Interface Components 📦 514

Version Control 📦 30

Virtualization 📦 71

Web Browsers 📦 42

Web Servers 📦 26

Web User Interface 📦 210