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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
  • seqr-loading-pipelines Public

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

    Python 23 MIT 20 22 6 Updated Mar 18, 2025
  • broad-epi-workflows-collection Public

    This repo contains WDL workflows written by the Epigenomics program.

    Jupyter Notebook 0 MIT 0 0 0 Updated Mar 18, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    Python 7 BSD-2-Clause 1 0 10 Updated Mar 18, 2025
  • cromwell Public

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

    Scala 1,012 BSD-3-Clause 359 743 46 Updated Mar 18, 2025
  • dig-dug-portal Public
    Vue 2 BSD-3-Clause 1 1 0 Updated Mar 18, 2025
  • firecloud-orchestration Public
    Scala 31 BSD-3-Clause 4 0 7 Updated Mar 18, 2025
  • warp Public

    WDL Analysis Research Pipelines

    WDL 210 BSD-3-Clause 102 5 21 Updated Mar 18, 2025
  • single_cell_portal_core Public

    Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

    Ruby 67 BSD-3-Clause 26 0 2 Updated Mar 18, 2025
  • dsp-appsec-infrastructure-apps Public

    This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.

    Python 6 BSD-3-Clause 2 0 3 Updated Mar 18, 2025
  • dig-aggregator-methods Public

    Monorepo of methods implemented for the Aggregator

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