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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 623

  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 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 1k 377

Repositories

Showing 10 of 1436 repositories
  • 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 14 Updated Jan 7, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 197 AGPL-3.0 92 49 5 Updated Jan 7, 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 Jan 7, 2026
  • dig-aggregator-methods Public

    Monorepo of methods implemented for the Aggregator

    broadinstitute/dig-aggregator-methods’s past year of commit activity
    Python 1 BSD-3-Clause 2 0 8 Updated Jan 7, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 224 BSD-3-Clause 112 6 10 Updated Jan 7, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 70 30 21 18 Updated Jan 7, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,900 623 1,272 (8 issues need help) 143 Updated Jan 7, 2026
  • ddp-angular Public

    Angular code for participant-facing pepper studies

    broadinstitute/ddp-angular’s past year of commit activity
    TypeScript 3 6 1 36 Updated Jan 7, 2026
  • genomeshader Public

    Visualization of biobank-scale genomic datasets.

    broadinstitute/genomeshader’s past year of commit activity
    HTML 4 BSD-3-Clause 0 7 (2 issues need help) 3 Updated Jan 7, 2026
  • poolq Public

    The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens

    broadinstitute/poolq’s past year of commit activity
    Scala 5 1 8 (1 issue needs help) 1 Updated Jan 7, 2026
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