Pacific Biosciences (PacBio) is an award-winning biotechnology company that manufactures instruments for genome sequencing. PacBio offers three complementary sequencing platforms: SequelIIe and Revio, which deliver accurate long read sequencing, and Onso, which offers high-throughput short read sequencing. PacBio has a large and growing international customer base, who are using these unique technologies to advance research in diverse fields, including human health and agriculture.
Each genome generates large volumes of raw sequencing data, which need to be processed through computationally intensive bioinformatics pipelines in order to produce actionable data, like genome assemblies and variant calls, that can inform research and clinical care. PacBio recognized a need to offer its customers a simple way to run best practices bioinformatics pipelines on their data. They designed their pipelines to be: (1) portable, so that they can be run in commercial cloud platforms as well as on premises, (2) sovereign, so that they can be run in customer environments in any geographic region, (3) human readable, so they are easy to maintain and extend, and (4) engine agnostic, so that customers have optionality to run using their preferred engine. PacBio sought a partner to ensure they delivered on this need.
PacBio partnered with Bioinformatics Services from Omics AI to test the deployment of the PacBio best practices Workflow Description Language (WDL) pipelines. By deploying onto Workbench PacBio could be confident customers would have easy access to these new pipelines. PacBio also requested a comprehensive framework to be developed for testing, publishing and running pipelines on Workbench, with emphasis on quality and ease of use.