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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 619

  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 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 1k 375

Repositories

Showing 10 of 1421 repositories
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 195 AGPL-3.0 91 50 5 Updated Nov 19, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 195 BSD-3-Clause 75 93 26 Updated Nov 19, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 26 BSD-3-Clause 4 0 5 Updated Nov 19, 2025
  • broad-epi-workflows-collection Public

    This repo contains WDL workflows written by the Epigenomics program.

    broadinstitute/broad-epi-workflows-collection’s past year of commit activity
    Jupyter Notebook 1 MIT 1 0 0 Updated Nov 19, 2025
  • depmap_omics_upload Public

    Subset and upload data to taiga for DepMap data releases

    broadinstitute/depmap_omics_upload’s past year of commit activity
    Python 0 Unlicense 0 0 1 Updated Nov 19, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 2 1 0 Updated Nov 19, 2025
  • 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 11 Updated Nov 19, 2025
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 220 BSD-3-Clause 111 6 11 Updated Nov 19, 2025
  • trexplorer-catalog Public

    Genome-wide TR catalog and variation clusters described in [Weisburd, Dolzhenko, et al. 2024]

    broadinstitute/trexplorer-catalog’s past year of commit activity
    Python 17 MIT 1 0 0 Updated Nov 19, 2025
  • 2025_varchamp_snakemake Public
    broadinstitute/2025_varchamp_snakemake’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Nov 19, 2025
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