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@broadinstitute

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 1.8k 597

  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 994 372

  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 359

Repositories

Showing 10 of 1337 repositories
  • depmap_omics Public

    What you need to process the Quarterly DepMap-Omics releases from Terra

    broadinstitute/depmap_omics’s past year of commit activity
    HTML 114 22 3 4 Updated Jan 29, 2025
  • shared-workflows Public

    GitHub Action workflows that can be shared by multiple repositories

    broadinstitute/shared-workflows’s past year of commit activity
    0 BSD-3-Clause 1 3 0 Updated Jan 29, 2025
  • bits-appengine Public

    BITS AppEngine Python Package

    broadinstitute/bits-appengine’s past year of commit activity
    Python 0 0 0 0 Updated Jan 29, 2025
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 8 Updated Jan 29, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 7 BSD-2-Clause 1 0 10 Updated Jan 29, 2025
  • dsp-appsec-infrastructure-apps Public

    This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.

    broadinstitute/dsp-appsec-infrastructure-apps’s past year of commit activity
    Python 6 BSD-3-Clause 2 0 4 Updated Jan 29, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 182 AGPL-3.0 89 54 4 Updated Jan 29, 2025
  • Bb_pangenome Public

    All required code and data for pangenomic analysis of Borrelia burgdorferi. Lemieux Lab 2025.

    broadinstitute/Bb_pangenome’s past year of commit activity
    1 0 0 0 Updated Jan 29, 2025
  • depmap-omics-long-read-rna Public
    broadinstitute/depmap-omics-long-read-rna’s past year of commit activity
    Python 0 0 0 0 Updated Jan 29, 2025
  • ega_submissions Public
    broadinstitute/ega_submissions’s past year of commit activity
    Python 0 0 0 0 Updated Jan 29, 2025
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