The Top 116 Genomics Open Source Projects

Awesome Open Source

Awesome Open Source

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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 116 Genomics Open Source Projects

Categories > Science > Genomics

Biopython ⭐ 2,799

Official git repository for Biopython (originally converted from CVS)

Deepvariant ⭐ 2,308

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

Deep Review ⭐ 1,162

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 ⭐ 1,013

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 ⭐ 672

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

Ncbi Genome Download ⭐ 540

Scripts to download genomes from the NCBI FTP servers

Deeptools ⭐ 472

Tools to process and analyze deep sequencing data.

Bwa Mem2 ⭐ 455

The next version of bwa-mem

Biojava ⭐ 452

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

Goatools ⭐ 444

Python library to handle Gene Ontology (GO) terms

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

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

Jbrowse ⭐ 405

A modern genome browser built with JavaScript and HTML5.

Bowtie2 ⭐ 390

A fast and sensitive gapped read aligner

Megahit ⭐ 361

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

Gwa_tutorial ⭐ 355

A comprehensive tutorial about GWAS and PRS

A high-performance, Pythonic language for bioinformatics

Jvarkit ⭐ 328

Java utilities for Bioinformatics

Pyfaidx ⭐ 316

Efficient pythonic random access to fasta subsequences

Postgui ⭐ 301

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

Arvados ⭐ 286

An open source platform for managing and analyzing biomedical big data

Eggnog Mapper ⭐ 285

Fast genome-wide functional annotation through orthology assignment

Haplotype VCF comparison tools

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

cython + htslib == fast VCF and BCF processing

Vcfanno ⭐ 264

annotate a VCF with other VCFs/BEDs/tabixed files

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Canvasxpress ⭐ 250

JavaScript VisualizationTools

Pyranges ⭐ 248

Performant Pythonic GenomicRanges

Dragonn ⭐ 234

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

Minigraph ⭐ 230

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

An ultrafast memory-efficient short read aligner

Genomeworks ⭐ 229

SDK for GPU accelerated genome assembly and analysis

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

🔬 BEDOPS: high-performance genomic feature operations

Octopus ⭐ 224

Bayesian haplotype-based mutation calling

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

Miniasm ⭐ 222

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

Higlass ⭐ 221

Fast large scale matrix visualization for the web.

Sequenceserver ⭐ 214

Intuitive local web frontend for the BLAST bioinformatics tool

Flowcraft ⭐ 214

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

Intermine ⭐ 206

A powerful open source data warehouse system

Genometools ⭐ 202

GenomeTools genome analysis system.

Ideogram ⭐ 202

Chromosome visualization for the web

Deep learning infrastructure for genomics

Rapid large-scale prokaryote pan genome analysis

Deep Rules ⭐ 194

Ten Quick Tips for Deep Learning in Biology

A genome browser that shows long reads and complex variants better

Reads simulator

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

Hifiasm ⭐ 178

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

An open-source toolkit for large-scale genomic analysis

Awesome Bioinformatics Benchmarks ⭐ 170

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

Viral Ngs ⭐ 161

Viral genomics analysis pipelines

Tools to work with variant call format files

Biomartr ⭐ 155

Genomic Data Retrieval with R

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

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

Snp Sites ⭐ 146

Finds SNP sites from a multi-FASTA alignment file

Artemis ⭐ 142

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

Somalier ⭐ 142

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

Miso Lims ⭐ 140

MISO: An open-source LIMS for NGS sequencing centres

variant expressions, annotation, and filtering for great good.

Circlator ⭐ 136

A tool to circularize genome assemblies

Benchmarking Tools ⭐ 135

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

Hts Nim ⭐ 134

nim wrapper for htslib for parsing genomics data files

Hicexplorer ⭐ 133

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

Kmer Cnt ⭐ 128

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

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

A cool place to store your Hi-C

NGLess: NGS with less work

Msprime ⭐ 117

Simulate genealogical trees and genomic sequence data using population genetic models

Genomics ⭐ 115

A collection of scripts and notes related to genomics and bioinformatics

Cgranges ⭐ 115

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

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

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

Smudgeplot ⭐ 110

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Antimicrobial Resistance Identification By Assembly

Genomicsqlite ⭐ 106

Genomics Extension for SQLite

Gcp For Bioinformatics ⭐ 103

GCP Essentials for Bioinformatics Researchers

Chipseq_pipeline ⭐ 100

AQUAS TF and histone ChIP-seq pipeline

Ga4gh Server ⭐ 93

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

Igv Snapshot Automator ⭐ 93

Script to automatically create and run IGV snapshot batchscripts

Pan-genome wide association studies

Bioinformatics library for .NET

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

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

Sibeliaz ⭐ 86

A fast whole-genome aligner based on de Bruijn graphs

Awesome 10x Genomics ⭐ 82

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

Bayesian genotyper for structural variants

Fastq.bio ⭐ 74

An interactive web tool for quality control of DNA sequencing data

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

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

Assembly Stats ⭐ 72

Get assembly statistics from FASTA and FASTQ files

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

1-100 of 116 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