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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 1.8k 597

  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 993 371

  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 360

Repositories

Showing 10 of 1334 repositories
  • gnomad-toolbox Public

    This repository provides a set of Python functions to simplify working with gnomAD Hail Tables. It includes tools for data access, filtering, and analysis.

    broadinstitute/gnomad-toolbox’s past year of commit activity
    Python 1 BSD-3-Clause 1 0 1 Updated Jan 21, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,750 597 1,231 (8 issues need help) 137 Updated Jan 21, 2025
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 61 28 23 17 Updated Jan 21, 2025
  • backstage Public

    Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)

    broadinstitute/backstage’s past year of commit activity
    TypeScript 2 0 5 4 Updated Jan 21, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 180 AGPL-3.0 89 54 5 Updated Jan 21, 2025
  • ddp-angular Public

    Angular code for participant-facing pepper studies

    broadinstitute/ddp-angular’s past year of commit activity
    TypeScript 3 4 1 32 Updated Jan 21, 2025
  • datarepo-helm Public

    A helm repo for Broad Data Science Platforms helm charts

    broadinstitute/datarepo-helm’s past year of commit activity
    Mustache 5 1 0 3 Updated Jan 21, 2025
  • hca-ingest-migration Public Forked from DataBiosphere/hca-ingest

    Working Repo for migration of HCA ingest from Dagster 0.12 to Dagster 1.8 (or 1.9)

    broadinstitute/hca-ingest-migration’s past year of commit activity
    Python 0 BSD-3-Clause 2 0 0 Updated Jan 21, 2025
  • ops-terra-utils Public
    broadinstitute/ops-terra-utils’s past year of commit activity
    Python 3 0 0 2 Updated Jan 21, 2025
  • genetic-prevalence-estimator Public
    broadinstitute/genetic-prevalence-estimator’s past year of commit activity
    Python 1 BSD-3-Clause 0 46 (4 issues need help) 4 Updated Jan 21, 2025
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