Skip to content
@broadinstitute

Broad Institute

Broad Institute of MIT and Harvard

Pinned Loading

  1. gatk gatk Public

    Official code repository for GATK versions 4 and up

    Java 1.8k 604

  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 1k 373

  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 361

Repositories

Showing 10 of 1375 repositories
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 186 AGPL-3.0 90 48 3 Updated Apr 15, 2025
  • single_cell_portal_core Public

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

    broadinstitute/single_cell_portal_core’s past year of commit activity
    Ruby 67 BSD-3-Clause 26 0 3 Updated Apr 15, 2025
  • dagster-utils Public

    Utilities and reusable patterns for using Dagster for Broad pipeline orchestration

    broadinstitute/dagster-utils’s past year of commit activity
    Python 4 BSD-3-Clause 0 0 1 Updated Apr 15, 2025
  • PANOPLY Public

    Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

    broadinstitute/PANOPLY’s past year of commit activity
    R 34 15 0 1 Updated Apr 15, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,791 604 1,244 (8 issues need help) 139 Updated Apr 15, 2025
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 211 BSD-3-Clause 102 5 12 Updated Apr 15, 2025
  • bibt-containers Public

    Public Docker containers for use with Blue Team tooling.

    broadinstitute/bibt-containers’s past year of commit activity
    Python 0 0 0 0 Updated Apr 15, 2025
  • firecloud-orchestration Public
    broadinstitute/firecloud-orchestration’s past year of commit activity
    Scala 31 BSD-3-Clause 4 0 2 Updated Apr 15, 2025
  • 2025_Grigoryan_Proteomics Public

    Repo for analysis of the Nomic Bio proteomics pilot data, collected as part of the OASIS Consortium

    broadinstitute/2025_Grigoryan_Proteomics’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 2 6 0 Updated Apr 15, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 8 BSD-2-Clause 1 0 8 Updated Apr 15, 2025
View all repositories

Top languages

Loading…

Most used topics

Loading…