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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 614

  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
  • stp_celldega_landscape_files Public
    broadinstitute/stp_celldega_landscape_files’s past year of commit activity
    WDL 0 0 0 0 Updated Sep 4, 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 0 Updated Sep 4, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,847 614 1,264 (8 issues need help) 141 Updated Sep 4, 2025
  • str-analysis Public

    Scripts and utilities related to analyzing short tandem repeats (STRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 39 MIT 9 0 0 Updated Sep 3, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 4 Updated Sep 3, 2025
  • sam Public

    workbench identity and access management

    broadinstitute/sam’s past year of commit activity
    Scala 41 BSD-3-Clause 12 3 7 Updated Sep 3, 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 22 24 4 Updated Sep 3, 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 3, 2025
  • palantir-workflows Public

    Utility workflows for the DSP hydro.gen team (formerly palantir)

    broadinstitute/palantir-workflows’s past year of commit activity
    WDL 26 BSD-3-Clause 9 4 1 Updated Sep 3, 2025
  • cellpainting-gallery Public

    Cell Painting Gallery

    broadinstitute/cellpainting-gallery’s past year of commit activity
    104 14 10 3 Updated Sep 3, 2025
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