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The Top 1,027 Genomics Open Source Projects on Github

Categories > Science > Genomics
Biopython ⭐ 2,978
Official git repository for Biopython (originally converted from CVS)
Deepvariant ⭐ 2,423
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Deep Review ⭐ 1,186
A collaboratively written review paper on deep learning, genomics, and precision medicine
Gatk ⭐ 1,162
Official code repository for GATK versions 4 and up
Minimap2 ⭐ 1,117
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Bwa ⭐ 1,011
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Galaxy ⭐ 910
Data intensive science for everyone.
Adam ⭐ 908
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Vg ⭐ 785
tools for working with genome variation graphs
Hail ⭐ 773
Scalable genomic data analysis.
Nucleus ⭐ 675
Python and C++ code for reading and writing genomics data.
Seq ⭐ 580
A high-performance, Pythonic language for bioinformatics
Ncbi Genome Download ⭐ 576
Scripts to download genomes from the NCBI FTP servers
Bwa Mem2 ⭐ 484
The next version of bwa-mem
Biojava ⭐ 474
📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Goatools ⭐ 473
Python library to handle Gene Ontology (GO) terms
Deeptools ⭐ 469
Tools to process and analyze deep sequencing data.
Jcvi ⭐ 467
Python library to facilitate genome assembly, annotation, and comparative genomics
Vcflib ⭐ 460
C++ library and cmdline tools for parsing and manipulating VCF files
Bowtie2 ⭐ 417
A fast and sensitive gapped read aligner
Jbrowse ⭐ 401
A modern genome browser built with JavaScript and HTML5.
Jvarkit ⭐ 352
Java utilities for Bioinformatics
Pyfaidx ⭐ 326
Efficient pythonic random access to fasta subsequences
Arvados ⭐ 301
An open source platform for managing and analyzing biomedical big data
Postgui ⭐ 301
A React web application to query and share any PostgreSQL database.
Maftools ⭐ 297
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
Eggnog Mapper ⭐ 292
Fast genome-wide functional annotation through orthology assignment
Hap.py ⭐ 283
Haplotype VCF comparison tools
Pyranges ⭐ 281
Performant Pythonic GenomicRanges
Delly ⭐ 278
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Cyvcf2 ⭐ 278
cython + htslib == fast VCF and BCF processing
Vcfanno ⭐ 271
annotate a VCF with other VCFs/BEDs/tabixed files
Megahit ⭐ 264
Ultra-fast and memory-efficient (meta-)genome assembler
Bio.jl ⭐ 255
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
Canvasxpress ⭐ 253
JavaScript VisualizationTools
Juicer ⭐ 250
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Octopus ⭐ 246
Bayesian haplotype-based mutation calling
Minigraph ⭐ 242
Proof-of-concept seq-to-graph mapper and graph generator
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Genomeworks ⭐ 235
SDK for GPU accelerated genome assembly and analysis
Higlass ⭐ 230
Fast, flexible and extensible genome browser.
Bowtie ⭐ 229
An ultrafast memory-efficient short read aligner
Htsjdk ⭐ 226
A Java API for high-throughput sequencing data (HTS) formats.
Sequenceserver ⭐ 225
Intuitive local web frontend for the BLAST bioinformatics tool
Bedops ⭐ 224
🔬 BEDOPS: high-performance genomic feature operations
Dragonn ⭐ 218
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
Intermine ⭐ 218
A powerful open source data warehouse system
Flowcraft ⭐ 214
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
Genometools ⭐ 213
GenomeTools genome analysis system.
Ideogram ⭐ 211
Chromosome visualization for the web
Janggu ⭐ 205
Deep learning infrastructure for genomics
Ribbon ⭐ 202
A genome browser that shows long reads and complex variants better
Deep Rules ⭐ 198
Ten Quick Tips for Deep Learning in Biology
Miniasm ⭐ 195
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
Wgsim ⭐ 188
Reads simulator
Glow ⭐ 185
An open-source toolkit for large-scale genomic analysis
Hifiasm ⭐ 185
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Gwa_tutorial ⭐ 184
A comprehensive tutorial about GWAS and PRS
Goleft ⭐ 184
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Vcfr ⭐ 168
Tools to work with variant call format files
Awesome Bioinformatics Benchmarks ⭐ 167
A curated list of bioinformatics bench-marking papers and resources.
Hgvs ⭐ 162
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Roary ⭐ 161
Rapid large-scale prokaryote pan genome analysis
Biomartr ⭐ 160
Genomic Data Retrieval with R
Somalier ⭐ 157
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Smoove ⭐ 154
structural variant calling and genotyping with existing tools, but, smoothly.
Miso Lims ⭐ 149
MISO: An open-source LIMS for NGS sequencing centres
Slivar ⭐ 149
variant expressions, annotation, and filtering for great good.
Circlator ⭐ 143
A tool to circularize genome assemblies
Hts Nim ⭐ 140
nim wrapper for htslib for parsing genomics data files
Sarek ⭐ 140
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Hicexplorer ⭐ 139
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Msprime ⭐ 129
Simulate genealogical trees and genomic sequence data using population genetic models
Viral Ngs ⭐ 129
Viral genomics analysis pipelines
Artemis ⭐ 127
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
Sarek ⭐ 126
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Neusomatic ⭐ 124
NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
Truvari ⭐ 124
Structural variant toolkit for VCFs
Ngless ⭐ 123
NGLess: NGS with less work
Genomics ⭐ 122
A collection of scripts and notes related to genomics and bioinformatics
Gcp For Bioinformatics ⭐ 119
GCP Essentials for Bioinformatics Researchers
Cooler ⭐ 117
A cool place to store your Hi-C
Qqman ⭐ 115
An R package for creating Q-Q and manhattan plots from GWAS results
Smudgeplot ⭐ 114
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Ariba ⭐ 112
Antimicrobial Resistance Identification By Assembly
Cgranges ⭐ 111
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
Benchmarking Tools ⭐ 110
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
Genomicsqlite ⭐ 110
Genomics Extension for SQLite
Kmer Cnt ⭐ 106
Code examples of fast and simple k-mer counters for tutorial purposes
Peddy ⭐ 104
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
Pathomicfusion ⭐ 103
Fusing Histology and Genomics via Deep Learning - IEEE TMI
Snp Sites ⭐ 101
Finds SNP sites from a multi-FASTA alignment file
Gfatools ⭐ 99
Tools for manipulating sequence graphs in the GFA and rGFA formats
Dram ⭐ 99
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Biowasm ⭐ 99
WebAssembly modules for genomics
Chipseq_pipeline ⭐ 97
AQUAS TF and histone ChIP-seq pipeline
Tidygenomics ⭐ 97
Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/
Bio ⭐ 97
Bioinformatics library for .NET
Aws Genomics Workflows ⭐ 96
Genomics Workflows on AWS
Exomiser ⭐ 95
A Tool to Annotate and Prioritize Exome Variants
1-100 of 1,027 projects

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Advertising 📦 9
All Projects
Application Programming Interfaces 📦 120
Applications 📦 181
Artificial Intelligence 📦 72
Blockchain 📦 70
Build Tools 📦 111
Cloud Computing 📦 79
Code Quality 📦 28
Collaboration 📦 30
Command Line Interface 📦 48
Community 📦 81
Companies 📦 60
Compilers 📦 60
Computer Science 📦 74
Configuration Management 📦 39
Content Management 📦 167
Control Flow 📦 197
Data Formats 📦 77
Data Processing 📦 266
Data Storage 📦 132
Economics 📦 60
Frameworks 📦 198
Games 📦 122
Graphics 📦 103
Hardware 📦 148
Integrated Development Environments 📦 47
Learning Resources 📦 147
Legal 📦 28
Libraries 📦 119
Lists Of Projects 📦 21
Machine Learning 📦 336
Mapping 📦 61
Marketing 📦 15
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Messaging 📦 97
Networking 📦 304
Operating Systems 📦 84
Operations 📦 120
Package Managers 📦 52
Programming Languages 📦 229
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Science 📦 42
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Software Quality 📦 127
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User Interface 📦 310
User Interface Components 📦 465
Version Control 📦 29
Virtualization 📦 68
Web Browsers 📦 38
Web Servers 📦 25
Web User Interface 📦 194
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