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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 603

  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 373

  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 361

Repositories

Showing 10 of 1362 repositories
  • starrynight Public

    Library and tools to process optical pooled screening datasets

    broadinstitute/starrynight’s past year of commit activity
    Python 2 BSD-3-Clause 0 25 2 Updated Apr 4, 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 20 23 3 Updated Apr 4, 2025
  • 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 Apr 4, 2025
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 144 BSD-3-Clause 25 95 (2 issues need help) 26 Updated Apr 3, 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 1,011 BSD-3-Clause 361 745 48 Updated Apr 3, 2025
  • firecloud-orchestration Public
    broadinstitute/firecloud-orchestration’s past year of commit activity
    Scala 31 BSD-3-Clause 4 0 3 Updated Apr 3, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 26 BSD-3-Clause 4 0 8 Updated Apr 3, 2025
  • 2021_09_01_VarChAMP_CellProfiler_Pipeline Public

    Instructions and recipes to run Distributed CellProfiler for processing VarChAMP variant painting images in the CS lab.

    broadinstitute/2021_09_01_VarChAMP_CellProfiler_Pipeline’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Apr 3, 2025
  • idmp-fungal-pipelines Public
    broadinstitute/idmp-fungal-pipelines’s past year of commit activity
    WDL 0 GPL-3.0 0 0 0 Updated Apr 3, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,787 603 1,240 (8 issues need help) 139 Updated Apr 3, 2025
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