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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 615

  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 1406 repositories
  • 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 1,034 BSD-3-Clause 374 756 55 Updated Sep 12, 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 8 Updated Sep 12, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 193 BSD-3-Clause 77 88 31 Updated Sep 12, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 6 Updated Sep 12, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 16 1 1 42 Updated Sep 12, 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 12, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 194 AGPL-3.0 90 53 3 Updated Sep 12, 2025
  • malaria Public
    broadinstitute/malaria’s past year of commit activity
    R 1 MIT 0 0 0 Updated Sep 12, 2025
  • dig-aggregator-methods Public

    Monorepo of methods implemented for the Aggregator

    broadinstitute/dig-aggregator-methods’s past year of commit activity
    Python 1 BSD-3-Clause 2 0 8 Updated Sep 12, 2025
  • PANOPLY Public

    Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

    broadinstitute/PANOPLY’s past year of commit activity
    R 37 16 0 1 Updated Sep 12, 2025
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