Official code repository for GATK versions 4 and up
☆1,921Mar 27, 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.☆1,054Updated this week
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,720Mar 22, 2025Updated last year
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,867Mar 18, 2026Updated last week
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆851Updated this week
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,308Mar 22, 2026Updated last week
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.☆3,667Mar 19, 2026Updated last week
- The next version of bwa-mem☆825Oct 15, 2025Updated 5 months ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,144Feb 13, 2026Updated last month
- Strelka2 germline and somatic small variant caller☆390Dec 29, 2021Updated 4 years ago
- Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale product…☆1,057Updated this week
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆865Feb 8, 2026Updated last month
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆541Updated this week
- Structural variant and indel caller for mapped sequencing data☆461Oct 11, 2025Updated 5 months ago
- Tools for working with SAM/BAM data☆607Dec 22, 2024Updated last year
- Wordpress hosting with auto-scaling on Cloudways • AdFully Managed hosting built for WordPress-powered businesses that need reliable, auto-scalable hosting. Cloudways SafeUpdates now available.
- bedtools - the swiss army knife for genome arithmetic☆1,027Mar 11, 2025Updated last year
- Copy number variant detection from targeted DNA sequencing☆606Mar 11, 2026Updated 2 weeks ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆721Mar 19, 2026Updated last week
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆508Feb 26, 2026Updated last month
- C library for high-throughput sequencing data formats☆913Mar 18, 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.☆551May 15, 2025Updated 10 months ago
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,532Feb 27, 2026Updated last month
- Workflows for germline short variant discovery with GATK4☆139May 7, 2021Updated 4 years ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,433Updated this week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools☆161Aug 10, 2022Updated 3 years ago
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆415Mar 13, 2026Updated 2 weeks ago
- Toolkit for processing sequences in FASTA/Q formats☆1,532Jun 1, 2025Updated 9 months ago
- Cloud-native genomic dataframes and batch computing☆1,051Updated this week
- A fast and sensitive gapped read aligner☆779Mar 7, 2026Updated 3 weeks ago
- A structural variation pipeline for short-read sequencing☆201Updated 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).☆847Mar 18, 2026Updated last week
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆334May 27, 2025Updated 10 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆833Feb 10, 2026Updated last month
- 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☆669Mar 20, 2026Updated last week
- VarDict☆203Jan 5, 2024Updated 2 years ago
- ☆303Mar 9, 2026Updated 2 weeks ago
- RNA-seq aligner☆2,162Mar 18, 2025Updated last year
- Haplotype VCF comparison tools☆462Dec 7, 2023Updated 2 years ago