Broad Institute

gatk

Official code repository for GATK versions 4 and up

warp

Warp Analysis Research Pipelines

gatk-sv

A structural variation pipeline for short-read sequencing

long-read-pipelines

Long read production pipelines

single_cell_portal_core

Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

python-cert_manager

Python interface to the Sectigo Certificate Manager REST API

palantir-workflows

Utility workflows for the DSP hydro.gen team (formerly palantir)

rawls

Rawls service for DSDE

seqr-loading-pipelines

hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

celldega

Spatial omics analysis and visualization library

exome-results-browsers

Results browsers for case-control studies of psychiatric diseases done at the Broad Institute

warp-tools

This repository contains all containers that WARP uses.

depmap-portal

Code for the DepMap portal at depmap.org

python-sudoers

Python library for parsing a Linux sudoers file

gnomad_chets

Phase of compound heterozygotes in gnomAD

seqr-helm

Helm charts for the seqr project

backstage

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

CNV-Mag

A Tool to Visualize CNV Events in WGS Data

dig-dug-portal

dig-aggregator-methods

Monorepo of methods implemented for the Aggregator

gnomad-deployments

kustomizations for current gnomad project kubernetes deployments

genetics-kp-dev

bits-appengine

BITS AppEngine Python Package

depmap-omics-rna

genemasker

mad4hatter_wdls

Repo for conversion of mad4hatter pipelines

shared-workflows

GitHub Action workflows that can be shared by multiple repositories

terraform-broad-redirect

Terraform configuration for the broad-redirect projects

terraform-google-redirect

Terraform module to create HTTP redirects using GCP components

watt

WDL Automated Testing Tool