Skip to content
@broadinstitute

Broad Institute

Broad Institute of MIT and Harvard

Pinned Loading

  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 376

  3. cromwell Public

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

    Scala 1k 366

Repositories

Showing 10 of 1388 repositories
  • starrynight Public

    Library and tools to process optical pooled screening datasets

    Python 6 BSD-3-Clause 4 27 3 Updated Jun 7, 2025
  • warp Public

    WDL Analysis Research Pipelines

    WDL 211 BSD-3-Clause 104 5 15 Updated Jun 7, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    Java 1,812 604 1,255 (8 issues need help) 141 Updated Jun 7, 2025
  • juniper Public
    Java 9 BSD-3-Clause 5 0 11 Updated Jun 7, 2025
  • dig-misc-projects Public

    Repository for miscellaneous DRG projects

    Python 0 0 0 0 Updated Jun 7, 2025
  • Drop-seq Public

    Java tools for analyzing Drop-seq data

    Java 128 MIT 35 13 1 Updated Jun 7, 2025
  • palantir-workflows Public

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

    WDL 26 BSD-3-Clause 9 4 2 Updated Jun 7, 2025
  • viral-pipelines Public

    viral-ngs: complete pipelines

    WDL 63 28 24 17 Updated Jun 7, 2025
  • seqr-loading-pipelines Public

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

    Python 23 MIT 20 26 4 Updated Jun 7, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    Python 188 AGPL-3.0 90 56 6 Updated Jun 6, 2025
View all repositories