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clinsv

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

cnvkit-dnanexus

DNAnexus app for CNVkit

eigensoft

Experimental EIGENSOFT performance improvements.

five-dollar-genome-analysis-pipeline

Workflows used for germline short variant discovery in WGS data

gangstr

A tool for profiling long STRs from short reads

gatk4-exome-analysis-pipeline

This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.

gatk4-genome-processing-pipeline

Workflows used for processing whole genome sequence data + germline variant calling.

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

hawk

Hitting associations with k-mers

oidc

Make XWiki an identity provider that can be reused by any application

pa-cwl-wes

Trigger CWL workflows via GA4GH WES and TES

pa-data-repository-service-schemas

A repository for the schemas used for the Data Repository Service.

pa-drs-crypt4gh-client

A DRS Client for the PA implementation of the DRS server incorporating Crypt4GH

pa-drs-crypt4gh-downloader

A tool to download Crypt4GH encrypted data from the PA DRS Server

pa-drs-crypt4gh-poc

A proof of concept of a DRS Server supporting Crypt4GH

pa-drs_ga4gh_starter_kit

Open, extensible server implementation of the GA4GH Data Repository Service (DRS) specification

pa-ga4gh-starter-kit-ui

Serves user interface for GA4GH starter kit microservices

pa-tesk

GA4GH Task Execution Service Root Project + Deployment scripts on Kubernetes

pa-tesk_api

GA4GH TES API Service that translates tasks into Kubernetes Batch API calls

pa-tesk_core

Python code that is launched as images into the Kubernetes cluster by tesk-api.

pa-tool-registry-service-schemas

APIs for discovering genomics tools, their metadata and their containers

pa-workflow-execution-service-schemas

The WES API is a standard way to run and manage portable workflows.

spliceai

A deep learning-based tool to identify splice variants

sso-devise-omniauth-provider

A devise Omniauth server which handles Single Sign On

xnat-openid-auth-plugin