title: A review of bioinformatic pipeline frameworks.
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.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Leipzig
mesh_terms: D019295:Computational Biology; D006801:Humans; D012984:Software
keywords: framework; pipeline; workflow