Official code repository for GATK versions 4 and up
☆1,965Jun 12, 2026Updated this week
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:
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,069Updated this week
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,749Mar 22, 2025Updated last year
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,914May 21, 2026Updated 3 weeks ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,376Jun 1, 2026Updated 2 weeks ago
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆872Jun 3, 2026Updated 2 weeks ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.☆3,727Mar 19, 2026Updated 2 months ago
- The next version of bwa-mem☆838Oct 15, 2025Updated 8 months ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,201May 19, 2026Updated 3 weeks ago
- Strelka2 germline and somatic small variant caller☆394Apr 20, 2026Updated last month
- Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale product…☆1,070Jun 11, 2026Updated last week
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆871Apr 20, 2026Updated last month
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆559Jun 10, 2026Updated last week
- Structural variant and indel caller for mapped sequencing data☆467Oct 11, 2025Updated 8 months ago
- Tools for working with SAM/BAM data☆610Dec 22, 2024Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- bedtools - the swiss army knife for genome arithmetic☆1,038Jun 10, 2026Updated last week
- Copy number variant detection from targeted DNA sequencing☆612Jun 9, 2026Updated last week
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆525Updated this week
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆743Jun 8, 2026Updated last week
- C library for high-throughput sequencing data formats☆925Jun 5, 2026Updated last week
- 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
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,570Jun 1, 2026Updated 2 weeks ago
- Workflows for germline short variant discovery with GATK4☆142May 7, 2021Updated 5 years ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,461Jun 10, 2026Updated last week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools☆162Aug 10, 2022Updated 3 years ago
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆417May 25, 2026Updated 3 weeks ago
- Toolkit for processing sequences in FASTA/Q formats☆1,542Jun 1, 2025Updated last year
- Cloud-native genomic dataframes and batch computing☆1,064Jun 9, 2026Updated last week
- A fast and sensitive gapped read aligner☆793Jun 1, 2026Updated 2 weeks ago
- A structural variation pipeline for short-read sequencing☆204Updated this week
- Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk…☆299Aug 22, 2018Updated 7 years ago
- Specification for the Workflow Description Language (WDL).☆852Updated this week
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆858May 2, 2026Updated last month
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆335May 27, 2025Updated last year
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆167Mar 28, 2023Updated 3 years ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆680Mar 20, 2026Updated 2 months ago
- VarDict☆204Jan 5, 2024Updated 2 years ago
- ☆308Mar 9, 2026Updated 3 months ago
- RNA-seq aligner☆2,208Mar 18, 2025Updated last year
- Haplotype VCF comparison tools☆469Dec 7, 2023Updated 2 years ago