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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 1.8k 597

  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 994 372

  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 359

Repositories

Showing 10 of 1334 repositories
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 16 Updated Jan 27, 2025
  • delphy Public

    Fast, scalable, accurate and accessible Bayesian phylogenetics

    broadinstitute/delphy’s past year of commit activity
    C++ 29 3 0 0 Updated Jan 27, 2025
  • EmmaEmb Public
    broadinstitute/EmmaEmb’s past year of commit activity
    Jupyter Notebook 4 MIT 0 0 0 Updated Jan 27, 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 65 BSD-3-Clause 26 0 0 Updated Jan 27, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 26 BSD-3-Clause 4 0 12 Updated Jan 27, 2025
  • sam Public

    workbench identity and access management

    broadinstitute/sam’s past year of commit activity
    Scala 42 BSD-3-Clause 12 3 28 Updated Jan 27, 2025
  • firecloud-orchestration Public
    broadinstitute/firecloud-orchestration’s past year of commit activity
    Scala 31 BSD-3-Clause 4 0 4 Updated Jan 27, 2025
  • cds-daintree Public
    broadinstitute/cds-daintree’s past year of commit activity
    Python 0 0 0 1 Updated Jan 27, 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 12 Updated Jan 27, 2025
  • gtex-pipeline Public

    GTEx & TOPMed data production and analysis pipelines

    broadinstitute/gtex-pipeline’s past year of commit activity
    Python 355 BSD-3-Clause 177 10 3 Updated Jan 27, 2025
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