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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 625

  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 382

  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 1470 repositories
  • lrma-aou2-panel-creation Public Forked from broadinstitute/lrma-aou1-panel-creation

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 2 long-reads callset.

    broadinstitute/lrma-aou2-panel-creation’s past year of commit activity
    Java 0 2 0 2 Updated Apr 15, 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 2 Updated Apr 15, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 202 BSD-3-Clause 76 98 30 Updated Apr 15, 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 3 0 9 Updated Apr 15, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 225 BSD-3-Clause 115 7 21 Updated Apr 15, 2026
  • pooled-cell-painting-image-processing Public
    broadinstitute/pooled-cell-painting-image-processing’s past year of commit activity
    Jupyter Notebook 6 BSD-3-Clause 4 16 1 Updated Apr 14, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,937 625 1,284 (8 issues need help) 146 Updated Apr 14, 2026
  • backstage Public

    Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)

    broadinstitute/backstage’s past year of commit activity
    TypeScript 2 0 0 3 Updated Apr 14, 2026
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 2 0 0 Updated Apr 14, 2026
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 169 GPL-3.0 24 33 (1 issue needs help) 25 Updated Apr 14, 2026
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