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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 987 369

  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 1324 repositories
  • gnomad-toolbox Public

    This repository provides a set of Python functions to simplify working with gnomAD Hail Tables. It includes tools for data access, filtering, and analysis.

    broadinstitute/gnomad-toolbox’s past year of commit activity
    Python 0 BSD-3-Clause 1 0 2 Updated Dec 11, 2024
  • delphy Public

    Fast, scalable, accurate and accessible Bayesian phylogenetics

    broadinstitute/delphy’s past year of commit activity
    C++ 28 3 0 0 Updated Dec 11, 2024
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 124 23 30 (1 issue needs help) 21 Updated Dec 11, 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 1,003 BSD-3-Clause 359 745 48 Updated Dec 11, 2024
  • 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 6 Updated Dec 11, 2024
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,728 594 1,224 (8 issues need help) 135 Updated Dec 11, 2024
  • dsp-reusable-workflows Public

    publicly available reusable workflows

    broadinstitute/dsp-reusable-workflows’s past year of commit activity
    Python 0 0 0 4 Updated Dec 11, 2024
  • ops-terra-utils Public
    broadinstitute/ops-terra-utils’s past year of commit activity
    Python 3 0 0 1 Updated Dec 11, 2024
  • 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 63 BSD-3-Clause 26 0 0 Updated Dec 11, 2024
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 203 BSD-3-Clause 98 7 17 Updated Dec 11, 2024
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