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@broadinstitute

Broad Institute

Broad Institute of MIT and Harvard

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  1. gatk Public

    Official code repository for GATK versions 4 and up

    Java 1.8k 602

  2. 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 1k 372

  3. 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 1353 repositories
  • dig-aggregator-methods Public

    Monorepo of methods implemented for the Aggregator

    Python 1 BSD-3-Clause 2 0 7 Updated Mar 18, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    Java 1,781 602 1,238 (8 issues need help) 133 Updated Mar 18, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    Jupyter Notebook 5 0 1 15 Updated Mar 18, 2025
  • viral-core Public

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

    Python 4 1 10 1 Updated Mar 18, 2025
  • viral-pipelines Public

    viral-ngs: complete pipelines

    WDL 61 28 24 18 Updated Mar 18, 2025
  • warp Public

    WDL Analysis Research Pipelines

    WDL 210 BSD-3-Clause 102 5 18 Updated Mar 18, 2025
  • gnomad-browser Public

    Explore gnomAD datasets on the web

    TypeScript 81 MIT 47 157 (3 issues need help) 15 Updated Mar 18, 2025
  • rawls Public

    Rawls service for DSDE

    Scala 26 BSD-3-Clause 4 0 14 Updated Mar 18, 2025
  • exome-results-browsers Public

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

    JavaScript 11 BSD-3-Clause 4 9 3 Updated Mar 17, 2025
  • palantir-workflows Public

    Utility workflows for the DSP hydro.gen team (formerly palantir)

    WDL 23 BSD-3-Clause 8 4 2 Updated Mar 18, 2025
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