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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 602

  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 998 372

  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 1349 repositories
  • gnomad-constraint Public
    broadinstitute/gnomad-constraint’s past year of commit activity
    Python 5 BSD-3-Clause 0 0 0 Updated Mar 13, 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 Mar 13, 2025
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 61 28 24 18 Updated Mar 13, 2025
  • seqr-loading-pipelines Public

    hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

    broadinstitute/seqr-loading-pipelines’s past year of commit activity
    Python 23 MIT 20 23 8 Updated Mar 13, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 182 BSD-3-Clause 75 78 22 Updated Mar 13, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 5 0 1 14 Updated Mar 13, 2025
  • 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 Mar 13, 2025
  • SpliceAI-lookup Public

    Website for checking SpliceAI and Pangolin scores:

    broadinstitute/SpliceAI-lookup’s past year of commit activity
    HTML 21 MIT 7 2 0 Updated Mar 13, 2025
  • starrynight Public

    Library and tools to process cell painting images

    broadinstitute/starrynight’s past year of commit activity
    Python 2 BSD-3-Clause 0 19 3 Updated Mar 13, 2025
  • sherlock Public

    DSP DevOps's deployment source-of-truth service

    broadinstitute/sherlock’s past year of commit activity
    Go 1 BSD-3-Clause 0 0 11 Updated Mar 13, 2025
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