Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
☆300Aug 22, 2018Updated 7 years ago
Alternatives and similar repositories for gatk
Users that are interested in gatk are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Official code repository for GATK versions 1.0 through 3.7 (full licensed package). For GATK 4 code, see the https://github.com/broadinst…☆147Aug 22, 2018Updated 7 years ago
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,066Jun 13, 2026Updated 3 weeks ago
- Official code repository for GATK versions 4 and up☆1,970Updated this week
- Assembly Based ReAligner☆75May 24, 2018Updated 8 years ago
- miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.☆181Nov 26, 2018Updated 7 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Integrated Variant Caller☆17Mar 15, 2018Updated 8 years ago
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,918Jun 25, 2026Updated last week
- Note: tabix and bgzip binaries are now part of the HTSlib project.☆92Aug 3, 2021Updated 4 years ago
- vcf file manipulation☆22Jul 9, 2015Updated 10 years ago
- Torrent Mapping Alignment Program☆20Mar 2, 2013Updated 13 years ago
- normalize, left-align, trim, validate and clean VCF files☆20Jul 22, 2015Updated 10 years ago
- Reference-based compression of SRA data☆40Mar 26, 2013Updated 13 years ago
- Convert genetic variants to minimal representation☆23Dec 8, 2017Updated 8 years ago
- FermiKit small variant calls for public SGDP samples☆17Sep 22, 2016Updated 9 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- C++ API & command-line toolkit for working with BAM data☆430May 18, 2025Updated last year
- Canvas - Copy number variant (CNV) calling from DNA sequencing data☆129Apr 20, 2026Updated 2 months ago
- Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead☆32Aug 16, 2017Updated 8 years ago
- Documenting usage and experience with bioinformatic tools☆40Sep 11, 2015Updated 10 years ago
- Scalable gVCF merging and joint variant calling for population sequencing projects☆185Apr 12, 2024Updated 2 years ago
- Browser for ExAC consortium data☆106Jan 21, 2022Updated 4 years ago
- Documentation for data model of ClinGen☆11Jul 5, 2018Updated 8 years ago
- A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.☆559May 15, 2025Updated last year
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,030Aug 24, 2024Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- A Java API for high-throughput sequencing data (HTS) formats.☆300Jun 15, 2026Updated 3 weeks ago
- Prioritize structural variants based on CADD scores☆29May 7, 2020Updated 6 years ago
- a simple C++ library for parsing and manipulating VCF files, + many command-line utilities☆20Mar 22, 2017Updated 9 years ago
- A tool to call somatic single nucleotide variants.☆41Aug 21, 2015Updated 10 years ago
- cython + htslib == fast VCF and BCF processing☆445Jun 25, 2026Updated last week
- A flexible framework for rapid genome analysis and interpretation☆320Oct 18, 2022Updated 3 years ago
- A powerful toolset for genome arithmetic.☆143May 28, 2021Updated 5 years ago
- Random collection of bioinformatics thingies☆19Mar 13, 2016Updated 10 years ago
- Tools for early stage alignment file processing☆96Mar 12, 2019Updated 7 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆227Sep 18, 2025Updated 9 months ago
- bedtools - the swiss army knife for genome arithmetic☆1,040Jun 10, 2026Updated 3 weeks ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆746Jul 1, 2026Updated last week
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆873Apr 20, 2026Updated 2 months ago
- Haplotype VCF comparison tools☆470Dec 7, 2023Updated 2 years ago
- de novo sequence assembler using string graphs☆244Aug 8, 2019Updated 6 years ago
- Tools for working with SAM/BAM data☆612Dec 22, 2024Updated last year