DOI: 10.1101/509455Jan 2, 2019Paper

BioSAILs: versatile workflow management for high-throughput data analysis

BioRxiv : the Preprint Server for Biology
Jillian RoweKristin Gunsalus

Abstract

Motivation: High-throughput analysis in the current era of systems biology encompasses a range of analysis workflows for different applications, such as transcriptomics, epigenetics, variant discovery, de novo genome assembly, etc. Many research institutes house a genomics core facility that is responsible for generating high-throughput sequencing data and often includes a core bioinformatics team that carries out data analysis. Core teams must both keep track of data and maintain numerous software packages and databases, which must be scalable according to ever-changing research needs, and they must allocate computational resources to them. Typical data analysis pipelines involve multiple software packages and require the ability to install, execute, and maintain software stacks on a variety of hardware/operating system configurations, including high-performance computing (HPC) facilities, stand-alone servers, and Cloud services. At the same time, individual researchers need to analyze their data and share their analysis steps with collaborators. Having to rely on ad hoc scripts and rigid internally developed pipelines is inefficient, difficult to track and maintain, and ultimately, limits the ability to adapt and evolve as re...Continue Reading

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