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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 612

  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 380

  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 373

Repositories

Showing 10 of 1406 repositories
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 147 BSD-3-Clause 25 95 (2 issues need help) 26 Updated Sep 3, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 193 BSD-3-Clause 77 87 33 Updated Sep 3, 2025
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 215 BSD-3-Clause 111 5 10 Updated Sep 3, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,845 612 1,264 (8 issues need help) 140 Updated Sep 3, 2025
  • lrma-aou1-panel-creation Public

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.

    broadinstitute/lrma-aou1-panel-creation’s past year of commit activity
    WDL 1 2 22 2 Updated Sep 3, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 193 AGPL-3.0 90 60 4 Updated Sep 2, 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 10 Updated Sep 2, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 2 1 0 Updated Sep 2, 2025
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 2 2 1 Updated Sep 2, 2025
  • firecloud-orchestration Public
    broadinstitute/firecloud-orchestration’s past year of commit activity
    Scala 31 BSD-3-Clause 4 0 3 Updated Sep 3, 2025
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