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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 1.7k 594

  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 984 368

  3. cromwell cromwell Public

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

    Scala 999 361

Repositories

Showing 10 of 1319 repositories
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 7 BSD-2-Clause 1 0 7 Updated Nov 24, 2024
  • broadinstitute/stp_segmentation_wdl’s past year of commit activity
    WDL 0 0 0 0 Updated Nov 23, 2024
  • 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 22 MIT 20 31 (1 issue needs help) 5 Updated Nov 23, 2024
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 202 BSD-3-Clause 96 7 13 Updated Nov 23, 2024
  • heimdall Public
    broadinstitute/heimdall’s past year of commit activity
    Shell 0 0 0 0 Updated Nov 23, 2024
  • juniper0 Public

    Preliminary Version of JUNIPER: Large-Scale Outbreak Reconstruction

    broadinstitute/juniper0’s past year of commit activity
    R 2 MIT 0 0 0 Updated Nov 23, 2024
  • molecular-data-provider Public

    Molecular Data Provider

    broadinstitute/molecular-data-provider’s past year of commit activity
    Python 11 MIT 8 3 5 Updated Nov 22, 2024
  • lembic Public

    Distilling some data for CFDE

    broadinstitute/lembic’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Nov 22, 2024
  • 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 999 BSD-3-Clause 361 744 48 Updated Nov 22, 2024