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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 624

  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 380

Repositories

Showing 10 of 1452 repositories
  • anvil_tdr_ingest Public

    Resources related to ingesting AnVIL datasets into Terra Data Repository

    broadinstitute/anvil_tdr_ingest’s past year of commit activity
    Jupyter Notebook 1 2 0 1 Updated Mar 3, 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 Mar 3, 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 10 Updated Mar 3, 2026
  • scp-ingest-pipeline Public

    File Ingest Pipeline for Single Cell Portal

    broadinstitute/scp-ingest-pipeline’s past year of commit activity
    Jupyter Notebook 5 BSD-3-Clause 0 0 1 Updated Mar 3, 2026
  • dcc_pigean_flask Public

    Flask server for the Pigean method

    broadinstitute/dcc_pigean_flask’s past year of commit activity
    Python 0 0 4 12 Updated Mar 3, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 225 BSD-3-Clause 112 7 11 Updated Mar 3, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,913 624 1,281 (8 issues need help) 148 Updated Mar 3, 2026
  • all-by-all-aou-browser Public
    broadinstitute/all-by-all-aou-browser’s past year of commit activity
    TypeScript 0 0 0 4 Updated Mar 3, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 201 BSD-3-Clause 76 97 26 Updated Mar 3, 2026
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 5 5 3 Updated Mar 3, 2026
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