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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 604

  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 1375 repositories
  • single_cell_portal_core Public

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

    Ruby 68 BSD-3-Clause 27 0 2 Updated Apr 22, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    Jupyter Notebook 5 0 1 15 Updated Apr 22, 2025
  • gnomad-browser-toolkit Public

    Components for building genomic data browsers

    JavaScript 9 MIT 6 7 2 Updated Apr 22, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    Java 1,796 604 1,245 (8 issues need help) 140 Updated Apr 22, 2025
  • seqr-loading-pipelines Public

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

    Python 23 MIT 20 28 3 Updated Apr 22, 2025
  • pyops-service-toolkit Public

    Shared Python utilities that help with interacting with Terra, TDR, BigQuery, and GCP to name a few.

    Python 3 0 0 1 Updated Apr 22, 2025
  • gnomad_qc Public
    Jupyter Notebook 69 BSD-3-Clause 27 7 11 Updated Apr 22, 2025
  • tandem-repeat-explorer Public

    An online portal for exploring genome-wide TR catalogs

    HTML 0 MIT 0 0 0 Updated Apr 22, 2025
  • depmap-omics-long-read-rna Public
    Python 0 0 0 0 Updated Apr 22, 2025
  • 2025_04_13_OASIS_CellPainting Public

    Repo for OASIS Cell Painting data

    Python 0 BSD-3-Clause 1 3 0 Updated Apr 22, 2025
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