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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 607

  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 378

  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 1405 repositories
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,823 607 1,259 (8 issues need help) 141 Updated Jul 31, 2025
  • 2025_Grigoryan_Proteomics Public

    Analysis repository for cpg0037-oasis/nomic

    broadinstitute/2025_Grigoryan_Proteomics’s past year of commit activity
    Jupyter Notebook 0 2 5 0 Updated Jul 31, 2025
  • hidive Public
    broadinstitute/hidive’s past year of commit activity
    Rust 0 BSD-3-Clause 0 6 1 Updated Jul 31, 2025
  • anvil_tdr_ingest Public

    Resources related to ingesting AnVIL datasets into Terra Data Repository

    broadinstitute/anvil_tdr_ingest’s past year of commit activity
    Jupyter Notebook 1 2 0 1 Updated Jul 31, 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 Jul 31, 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 1 22 2 Updated Jul 31, 2025
  • ddp-study-server Public

    Pepper Study Server

    broadinstitute/ddp-study-server’s past year of commit activity
    Java 8 BSD-3-Clause 6 1 3 Updated Jul 31, 2025
  • ygramul Public

    Hierarchical knowledge graph for PIGEAN results

    broadinstitute/ygramul’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Jul 30, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 190 AGPL-3.0 90 55 2 Updated Jul 30, 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 1,025 BSD-3-Clause 373 754 53 Updated Jul 30, 2025
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