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Updated: Mar 23, 2026

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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A review of bioinformatic pipeline frameworks
Briefings in Bioinformatics
|March 26, 2016
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.

