A review of bioinformatic pipeline frameworks | Zendy

Jeremy Leipzig | Zendy

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A review of bioinformatic pipeline frameworks

Author(s) -

Jeremy Leipzig

Publication year - 2016

Publication title -

briefings in bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.204

H-Index - 113

eISSN - 1477-4054

pISSN - 1467-5463

DOI - 10.1093/bib/bbw020

Subject(s) - computer science , pipeline (software) , workbench , implementation , metadata , interface (matter) , software engineering , process (computing) , syntax , programming language , key (lock) , data mining , world wide web , artificial intelligence , operating system , bubble , maximum bubble pressure method , visualization

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.

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