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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 1.8k 604

  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 373

  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 362

Repositories

Showing 10 of 1375 repositories
  • starrynight Public

    Library and tools to process optical pooled screening datasets

    broadinstitute/starrynight’s past year of commit activity
    Jupyter Notebook 3 BSD-3-Clause 0 38 0 Updated Apr 23, 2025
  • pyops-service-toolkit Public

    Shared Python utilities that help with interacting with Terra, TDR, BigQuery, and GCP to name a few.

    broadinstitute/pyops-service-toolkit’s past year of commit activity
    Python 3 0 0 1 Updated Apr 23, 2025
  • ops-terra-utils Public
    broadinstitute/ops-terra-utils’s past year of commit activity
    Python 5 2 0 5 Updated Apr 23, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 187 BSD-3-Clause 75 82 22 Updated Apr 23, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,797 604 1,245 (8 issues need help) 139 Updated Apr 23, 2025
  • gnomad-browser-toolkit Public

    Components for building genomic data browsers

    broadinstitute/gnomad-browser-toolkit’s past year of commit activity
    JavaScript 9 MIT 6 7 2 Updated Apr 23, 2025
  • idmp-fungal-pipelines Public
    broadinstitute/idmp-fungal-pipelines’s past year of commit activity
    WDL 0 GPL-3.0 0 0 0 Updated Apr 23, 2025
  • tandem-repeat-explorer Public

    An online portal for exploring genome-wide TR catalogs

    broadinstitute/tandem-repeat-explorer’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Apr 23, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 8 BSD-2-Clause 1 0 8 Updated Apr 23, 2025
  • ddp-angular Public

    Angular code for participant-facing pepper studies

    broadinstitute/ddp-angular’s past year of commit activity
    TypeScript 3 4 1 34 Updated Apr 23, 2025
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