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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 603

  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 373

  3. cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    Scala 1k 361

Repositories

Showing 10 of 1358 repositories
  • SpliceAI-lookup Public

    Website for checking SpliceAI and Pangolin scores:

    HTML 22 MIT 7 2 0 Updated Mar 31, 2025
  • hidive Public
    Rust 0 BSD-3-Clause 0 5 1 Updated Mar 31, 2025
  • monorepo Public

    Compendium of tools for the Imaging Platform

    Python 11 BSD-3-Clause 2 7 0 Updated Mar 31, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    Java 1,784 603 1,239 (8 issues need help) 140 Updated Mar 31, 2025
  • bits-appengine Public

    BITS AppEngine Python Package

    Python 0 0 0 1 Updated Mar 31, 2025
  • sherlock Public

    DSP DevOps's deployment source-of-truth service

    Go 1 BSD-3-Clause 0 0 16 Updated Mar 31, 2025
  • epi-SHARE-seq-pipeline Public

    Epigenomics Program pipeline to analyze SHARE-seq data.

    WDL 20 MIT 3 28 0 Updated Mar 30, 2025
  • 2021_09_01_VarChAMP_CellProfiler_Pipeline Public

    Instructions and recipes to run Distributed CellProfiler for processing VarChAMP variant painting images in the CS lab.

    Jupyter Notebook 0 0 0 0 Updated Mar 30, 2025
  • seqr-helm Public

    Helm charts for the seqr project

    Python 3 BSD-3-Clause 2 0 0 Updated Mar 30, 2025
  • seqr-loading-pipelines Public

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

    Python 23 MIT 20 22 2 Updated Mar 29, 2025
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