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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 993 372

  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 1339 repositories
  • viral-core Public

    viral-ngs: read QC, barcode metrics, spike-in metrics, Illumina metrics and demux

    broadinstitute/viral-core’s past year of commit activity
    Python 4 1 10 1 Updated Feb 5, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 177 BSD-3-Clause 72 73 21 Updated Feb 4, 2025
  • BEClust3D Public
    broadinstitute/BEClust3D’s past year of commit activity
    Jupyter Notebook 0 0 0 8 Updated Feb 5, 2025
  • stp_segmentation_wdl Public
    broadinstitute/stp_segmentation_wdl’s past year of commit activity
    WDL 0 0 0 0 Updated Feb 5, 2025
  • carmen-analysis Public
    broadinstitute/carmen-analysis’s past year of commit activity
    Python 4 MIT 0 0 0 Updated Feb 5, 2025
  • Drop-seq Public

    Java tools for analyzing Drop-seq data

    broadinstitute/Drop-seq’s past year of commit activity
    Java 124 MIT 35 23 0 Updated Feb 5, 2025
  • terra-featured-workspace-tests Public

    This code is to test that terra featured workspaces are working properly

    broadinstitute/terra-featured-workspace-tests’s past year of commit activity
    Python 2 0 0 1 Updated Feb 5, 2025
  • hca-ingest-migration Public Forked from DataBiosphere/hca-ingest

    Working Repo for migration of HCA ingest from Dagster 0.12 to Dagster 1.8 (or 1.9)

    broadinstitute/hca-ingest-migration’s past year of commit activity
    Python 0 BSD-3-Clause 2 0 1 Updated Feb 5, 2025
  • ddp-angular Public

    Angular code for participant-facing pepper studies

    broadinstitute/ddp-angular’s past year of commit activity
    TypeScript 3 4 1 33 Updated Feb 5, 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 11 Updated Feb 5, 2025
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