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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 2k 628

  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 384

  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 381

Repositories

Showing 10 of 1541 repositories
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal's past year of commit activity
    Vue 3 BSD-3-Clause 4 0 8 Updated Oct 6, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr's past year of commit activity
    Python 219 AGPL-3.0 97 48 8 Updated Oct 6, 2026
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines's past year of commit activity
    Jupyter Notebook 152 BSD-3-Clause 25 95 (2 issues need help) 24 Updated Oct 6, 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 2 1 6 Updated Oct 6, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp's past year of commit activity
    Jupyter Notebook 231 BSD-3-Clause 119 13 23 Updated Oct 6, 2026
  • haplograph Public
    broadinstitute/haplograph's past year of commit activity
    WDL 3 MIT 0 0 0 Updated Oct 6, 2026
  • ml4h Public
    broadinstitute/ml4h's past year of commit activity
    Python 181 GPL-3.0 12 33 (1 issue needs help) 27 Updated Oct 6, 2026
  • site-shell Public
    broadinstitute/site-shell's past year of commit activity
    JavaScript 1 BSD-3-Clause 0 0 0 Updated Oct 6, 2026
  • warp-tools Public

    This repository contains all containers that WARP uses.

    broadinstitute/warp-tools's past year of commit activity
    Python 16 BSD-3-Clause 4 1 9 Updated Oct 6, 2026
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls's past year of commit activity
    Scala 27 BSD-3-Clause 3 0 10 Updated Oct 6, 2026
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