A review of bioinformatic pipeline frameworks. (24th March 2016)

• Record Type: Journal Article
• Authors: Leipzig, Jeremy
• Is Part Of: Briefings in bioinformatics. Volume 18:Number 3(2017:May)
• Page Start: 530
• Page End: 536
• Publication Date: 2016-03-24
• Subjects: pipeline -- workflow -- framework; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbw020
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Modern implementations of these frameworks differ on three key dimensions: using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface. Here I survey and compare the design philosophies of several current pipeline frameworks. I provide practical recommendations based on analysis requirements and the user base.