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 1.9k 623

  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 1.1k 381

  3. cromwell cromwell Public

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

    Scala 1.1k 378

Repositories

Showing 10 of 1450 repositories
  • bican-mccarroll-manuscript1 Public

    Scripts used to process data for the first McCarroll lab BICAN manuscript

    broadinstitute/bican-mccarroll-manuscript1’s past year of commit activity
    R 0 MIT 0 0 2 Updated Feb 25, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 73 30 22 20 Updated Feb 25, 2026
  • viral-ngs Public

    viral-ngs: command line tools and wrappers for processing raw viral genomic data

    broadinstitute/viral-ngs’s past year of commit activity
    Python 194 MIT 67 2 0 Updated Feb 25, 2026
  • DepMap-NextGen-Public Public
    broadinstitute/DepMap-NextGen-Public’s past year of commit activity
    Python 1 0 0 0 Updated Feb 25, 2026
  • cromwell Public

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

    broadinstitute/cromwell’s past year of commit activity
    Scala 1,053 BSD-3-Clause 378 759 49 Updated Feb 25, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 201 BSD-3-Clause 76 97 26 Updated Feb 25, 2026
  • permutect Public

    Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling

    broadinstitute/permutect’s past year of commit activity
    Python 9 1 10 2 Updated Feb 25, 2026
  • taigapy Public

    Library for reading from taiga in python

    broadinstitute/taigapy’s past year of commit activity
    Python 1 1 2 3 Updated Feb 25, 2026
  • hermitcrab Public

    Provision GCP instances along with PD for interactive development with visual studio code

    broadinstitute/hermitcrab’s past year of commit activity
    Python 4 BSD-2-Clause 2 0 0 Updated Feb 25, 2026
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 5 5 3 Updated Feb 25, 2026
View all repositories

Top languages

Loading…