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@broadinstitute

Broad Institute

Broad Institute of MIT and Harvard

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  1. gatk gatk Public

    Official code repository for GATK versions 4 and up

    Java 2k 632

  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 386

  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 382

Repositories

Showing 10 of 1547 repositories
  • bits-appengine Public

    BITS AppEngine Python Package

    broadinstitute/bits-appengine's past year of commit activity
    Python 0 0 0 0 Updated Oct 26, 2026
  • python-cert_manager Public

    Python interface to the Sectigo Certificate Manager REST API

    broadinstitute/python-cert_manager's past year of commit activity
    Python 43 BSD-3-Clause 22 2 0 Updated Oct 26, 2026
  • str-analysis Public

    Scripts and utilities for analyzing tandem repeats (TRs).

    broadinstitute/str-analysis's past year of commit activity
    Python 53 MIT 15 0 0 Updated Oct 25, 2026
  • molab-slurm Public

    SLURM's commands (sbatch, squeue, scancel, ...) for a molab box you cannot ssh into

    broadinstitute/molab-slurm's past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 25, 2026
  • PrimerCast Public

    Design tool for highly performant qPCR diagnostics.

    broadinstitute/PrimerCast's past year of commit activity
    Python 12 MIT 1 4 0 Updated Oct 25, 2026
  • mccarroll_tw_clp Public

    Command-line wrappers for twcli with validation

    broadinstitute/mccarroll_tw_clp's past year of commit activity
    Python 0 MIT 0 0 3 Updated Oct 25, 2026
  • mccarroll_nextflow Public

    Nextflow workflows for BICAN scRNA processing

    broadinstitute/mccarroll_nextflow's past year of commit activity
    Nextflow 2 MIT 0 10 3 Updated Oct 25, 2026
  • celldega Public

    Spatial and multiomic visualization and analysis library

    broadinstitute/celldega's past year of commit activity
    Jupyter Notebook 79 7 1 64 Updated Oct 25, 2026
  • poolq Public

    The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens

    broadinstitute/poolq's past year of commit activity
    Scala 6 1 8 (1 issue needs help) 1 Updated Oct 25, 2026
  • koina Public Forked from wilhelm-lab/koina

    Democratizing ML in proteomics

    broadinstitute/koina's past year of commit activity
    Jupyter Notebook 0 Apache-2.0 30 0 21 Updated Oct 25, 2026
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