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Broad Institute

Broad Institute of MIT and Harvard

1.1k followers
Cambridge, MA
http://www.broadinstitute.org/
@broadinstitute

Overview
Repositories 1.4k
Projects 2
Packages
People 33

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gatk Public

Official code repository for GATK versions 4 and up

Java 1.8k 608
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 379
cromwell Public

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

Scala 1k 373

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Showing 10 of 1406 repositories

gatk-sv Public
A structural variation pipeline for short-read sequencing

Python 191 BSD-3-Clause 77 86 28 Updated Aug 8, 2025
cromwell Public
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

Scala 1,025 BSD-3-Clause 373 755 54 Updated Aug 8, 2025
hidive Public

Rust 0 BSD-3-Clause 0 6 1 Updated Aug 8, 2025
ddp-study-server Public
Pepper Study Server

Java 8 BSD-3-Clause 6 1 2 Updated Aug 8, 2025
seqr-helm Public
Helm charts for the seqr project

Python 3 BSD-3-Clause 2 3 0 Updated Aug 8, 2025
seqr-loading-pipelines Public
hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

Python 23 MIT 22 25 3 Updated Aug 8, 2025
juniper Public

Java 9 BSD-3-Clause 5 0 16 Updated Aug 8, 2025
data-registry-api Public

Python 1 BSD-3-Clause 1 0 1 Updated Aug 7, 2025
depmap-portal Public
Code for the DepMap portal at depmap.org

Python 8 BSD-2-Clause 1 0 13 Updated Aug 7, 2025
single_cell_portal_core Public
Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

Ruby 68 BSD-3-Clause 27 0 1 Updated Aug 7, 2025

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ncats-translator gene-list-sharpener genomics carpenter-lab wdl

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