Evaluation of serverless computing for scalable execution of a joint variant calling workflow.

ABSTRACT: Advances in whole-genome sequencing have greatly reduced the cost and time of obtaining raw genetic information, but the computational requirements of analysis remain a challenge. Serverless computing has emerged as an alternative to using dedicated compute resources, but its utility has not been widely evaluated for standardized genomic workflows. In this study, we define and execute a best-practice joint variant calling workflow using the SWEEP workflow management system. We present an analysis of performance and scalability, and discuss the utility of the serverless paradigm for executing workflows in the field of genomics research. The GATK best-practice short germline joint variant calling pipeline was implemented as a SWEEP workflow comprising 18 tasks. The workflow was executed on I

SUBMITTER: John A 

PROVIDER: S-EPMC8270184 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature