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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 1.9k 616

  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 374

Repositories

Showing 10 of 1410 repositories
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 3 Updated Oct 15, 2025
  • single_cell_portal_core Public

    Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

    broadinstitute/single_cell_portal_core’s past year of commit activity
    Ruby 68 BSD-3-Clause 27 0 2 Updated Oct 15, 2025
  • cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    broadinstitute/cromwell’s past year of commit activity
    Scala 1,039 BSD-3-Clause 374 757 55 Updated Oct 15, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 195 AGPL-3.0 90 51 4 Updated Oct 15, 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 17 5 Updated Oct 15, 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 6 Updated Oct 15, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,859 616 1,268 (8 issues need help) 141 Updated Oct 15, 2025
  • stp_celldega_landscape_files Public
    broadinstitute/stp_celldega_landscape_files’s past year of commit activity
    Python 0 0 0 0 Updated Oct 15, 2025
  • dig-job-server Public
    broadinstitute/dig-job-server’s past year of commit activity
    Vue 0 0 0 0 Updated Oct 14, 2025
  • variant-curation-portal Public

    Web application for curating loss of function variants

    broadinstitute/variant-curation-portal’s past year of commit activity
    Python 4 MIT 1 46 2 Updated Oct 14, 2025
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