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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 602

  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 997 372

  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 1348 repositories
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 5 0 1 14 Updated Mar 5, 2025
  • seqr-loading-pipelines Public

    hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

    broadinstitute/seqr-loading-pipelines’s past year of commit activity
    Python 23 MIT 20 22 10 Updated Mar 5, 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 12 Updated Mar 4, 2025
  • mitograph Public
    broadinstitute/mitograph’s past year of commit activity
    Rust 0 0 0 0 Updated Mar 4, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,777 602 1,237 (8 issues need help) 134 Updated Mar 4, 2025
  • 2025_varchamp_snakemake Public
    broadinstitute/2025_varchamp_snakemake’s past year of commit activity
    Python 0 0 0 0 Updated Mar 4, 2025
  • hca-ingest-migration Public Forked from DataBiosphere/hca-ingest

    Working Repo for migration of HCA ingest from Dagster 0.12 to Dagster 1.8 (or 1.9)

    broadinstitute/hca-ingest-migration’s past year of commit activity
    Python 0 BSD-3-Clause 2 0 1 Updated Mar 4, 2025
  • BEClust3D Public
    broadinstitute/BEClust3D’s past year of commit activity
    Jupyter Notebook 0 0 0 8 Updated Mar 4, 2025
  • workbench-libs Public

    Workbench utility libraries

    broadinstitute/workbench-libs’s past year of commit activity
    Scala 9 4 0 3 Updated Mar 4, 2025
  • firecloud-orchestration Public
    broadinstitute/firecloud-orchestration’s past year of commit activity
    Scala 31 BSD-3-Clause 4 0 6 Updated Mar 4, 2025
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