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Broad Institute

Broad Institute of MIT and Harvard

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  1. gatk gatk Public

    Official code repository for GATK versions 4 and up

    Java 1.9k 622

  2. picard picard Public

    A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

    Java 1.1k 381

  3. cromwell cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    Scala 1.1k 379

Repositories

Showing 10 of 1447 repositories
  • taigapy Public

    Library for reading from taiga in python

    broadinstitute/taigapy’s past year of commit activity
    Python 1 1 2 3 Updated Feb 13, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 72 30 21 20 Updated Feb 13, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 200 AGPL-3.0 93 41 7 Updated Feb 13, 2026
  • warp-tools Public

    This repository contains all containers that WARP uses.

    broadinstitute/warp-tools’s past year of commit activity
    Python 12 BSD-3-Clause 3 1 4 Updated Feb 13, 2026
  • viral-ngs Public

    viral-ngs: command line tools and wrappers for processing raw viral genomic data

    broadinstitute/viral-ngs’s past year of commit activity
    Python 193 MIT 67 1 0 Updated Feb 13, 2026
  • gnomad_methods Public

    Hail helper functions for the gnomAD project and Translational Genomics Group

    broadinstitute/gnomad_methods’s past year of commit activity
    Python 100 MIT 31 9 9 Updated Feb 13, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,909 622 1,278 (8 issues need help) 144 Updated Feb 13, 2026
  • lattice Public
    broadinstitute/lattice’s past year of commit activity
    HTML 1 BSD-3-Clause 1 7 0 Updated Feb 13, 2026
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    TypeScript 8 BSD-2-Clause 1 1 7 Updated Feb 13, 2026
  • bican-mccarroll-manuscript1 Public

    Scripts used to process data for the first McCarroll lab BICAN manuscript

    broadinstitute/bican-mccarroll-manuscript1’s past year of commit activity
    R 0 MIT 0 0 2 Updated Feb 13, 2026
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