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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 599

  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 995 372

  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 360

Repositories

Showing 10 of 1344 repositories
  • gnomad_methods Public

    Hail helper functions for the gnomAD project and Translational Genomics Group

    broadinstitute/gnomad_methods’s past year of commit activity
    Python 92 MIT 29 7 7 Updated Feb 20, 2025
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 208 BSD-3-Clause 101 4 19 Updated Feb 20, 2025
  • dsp-reusable-workflows Public

    publicly available reusable workflows

    broadinstitute/dsp-reusable-workflows’s past year of commit activity
    Python 1 0 0 4 Updated Feb 20, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 0 0 Updated Feb 20, 2025
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 9 Updated Feb 20, 2025
  • DropSift Public

    cell caller for sn/snRNA sequence data

    broadinstitute/DropSift’s past year of commit activity
    R 0 0 0 0 Updated Feb 20, 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 7 Updated Feb 20, 2025
  • exome-results-browsers Public

    Results browsers for case-control studies of psychiatric diseases done at the Broad Institute

    broadinstitute/exome-results-browsers’s past year of commit activity
    JavaScript 11 BSD-3-Clause 4 7 3 Updated Feb 20, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 5 0 1 11 Updated Feb 20, 2025
  • lrma-aou1-panel-creation Public

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.

    broadinstitute/lrma-aou1-panel-creation’s past year of commit activity
    WDL 1 0 22 2 Updated Feb 20, 2025
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