seqr is a web-based analysis tool for rare disease genomics.

This repository contains the code that underlies the Broad seqr instance, as well as other seqr deployments.

seqr consists of the following components or micro-services:

• seqr - the main client-server application - javascript + react.js on the client-side, python + django on the server-side.
• postgres - SQL database used by seqr and phenotips to store project metadata and user-generated content such as variant notes, etc.
• phenotips - 3rd-party web-based tool for entering structured phenotype information.
• mongo - NoSQL database used to store variant callsets and reference data.
• matchbox - a service that encapsulates communication with the Match Maker Exchange.
• nginx - http server used as the main gateway between seqr and the internet.
• elasticsearch - NoSQL database alternative to mongo that currently supports loading large callsets using a Spark-based hail pipeline.
• kibana - (optional) dashboard and visual interface for elasticsearch.

Kubernetes-based Installation Instructions - The Kubernetes-based installation allows for fully scripted deployment of all seqr components. It supports local installation on any operating system using a virtualized environment (minikube) as well as cloud deployment on Google, AWS, and other clouds.

Manual Installation Instructions - walks through the steps to install all seqr components on MacOSX.

Data pre-processing and loading pipelines - hail pipelines for pre-processing and loading datasets into an elasticsearch datastore.

Please Note: seqr is still under active development, and undergoing refactoring. We suggest you contact us if you want to build on this repo.