Broad Genomics News

Broad Institute Partners with Illumina to Offer the Genome Analysis Toolkit Suite on BaseSpace Sequence Hub

CAMBRIDGE, Mass. April 6, 2016 – The Broad Institute of MIT and Harvard is partnering with Illumina, Inc. to provide cloud-based access to the latest version of its popular Genome Analysis Toolkit (GATK) through BaseSpace Sequence Hub, Illumina’s cloud-based platform for next-generation sequencing (NGS) data management and analysis. BaseSpace Hub is one of the world’s largest cloud-based genomic platforms and the only platform that seamlessly connects the sequencing instrument to the data. This partnership is enabled by an earlier announcement that the Broad Institute’s Software-as-a-Service (SaaS) mechanism will now be available on multiple clouds.

“By making the best practices version of GATK available to users of BaseSpace Hub, we aim to make it as convenient as possible for users to incorporate this tool into their workflows,” said Eric Banks, Senior Director of Data Sciences and Data Engineering at Broad and one of the creators of the GATK software package. “This builds on our recent efforts to expand access and give options to the 31,000 registered users of GATK by developing plans to make the software available in many clouds, as well as through the traditional on-premises mode.”

The BaseSpace Hub-hosted version of the GATK best practices pipeline will use Workflow Definition Language (WDL), a programming language developed at Broad to facilitate the movement of analytical pipelines to the cloud. This ensures that, as future versions of GATK are released, users of BaseSpace Hub will always be up to date. This also opens the door to other pipelines developed at Broad (e.g. somatic variant calling) being made available via BaseSpace Hub in the future.

“We are excited to offer the cloud-optimized version of the GATK Best Practices pipeline to the users of BaseSpace Sequence Hub,” said Brady Davis, Senior Director of Enterprise Informatics at Illumina. “The BaseSpace Hub user community represents a wide range of scientists who are pushing the limits of human disease research. This agreement ensures users have access to the most up to date tools for variant discovery.”