Broad Institute

Broad Institute of MIT and Harvard

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gatk gatk Public

Official code repository for GATK versions 4 and up

Java 2k 627
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 383
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

str-truth-set-v2 Public

broadinstitute/str-truth-set-v2’s past year of commit activity

Python 2 MIT 0 0 0 Updated Jul 8, 2026
str-truth-set Public
Genome-wide tandem repeat (TR) truth set based on the Synthetic Diploid Benchmark [Li et al. 2018]

broadinstitute/str-truth-set’s past year of commit activity

Python 7 MIT 0 0 0 Updated Jul 8, 2026
haplograph Public

broadinstitute/haplograph’s past year of commit activity

WDL 3 MIT 0 0 1 Updated Jul 8, 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 13 Apache-2.0 2 7 1 Updated Jul 8, 2026
gatk Public
Official code repository for GATK versions 4 and up

broadinstitute/gatk’s past year of commit activity

Java 1,972 627 1,289 (8 issues need help) 149 Updated Jul 8, 2026
geneset-extractor-dev Public
Geneset Extractor Development

broadinstitute/geneset-extractor-dev’s past year of commit activity

Shell 0 MIT 6 2 7 Updated Jul 7, 2026
str-analysis Public
Scripts and utilities for analyzing tandem repeats (TRs).

broadinstitute/str-analysis’s past year of commit activity

Python 46 MIT 14 0 0 Updated Jul 7, 2026
long-read-pipelines Public
Long read production pipelines

broadinstitute/long-read-pipelines’s past year of commit activity

Jupyter Notebook 151 BSD-3-Clause 24 95 (2 issues need help) 25 Updated Jul 7, 2026
seqr Public
web-based analysis tool for rare disease genomics

broadinstitute/seqr’s past year of commit activity

Python 211 AGPL-3.0 94 44 5 Updated Jul 7, 2026
dig-dug-portal Public

broadinstitute/dig-dug-portal’s past year of commit activity

HTML 3 BSD-3-Clause 2 0 1 Updated Jul 7, 2026

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