mi RP ursuit—a pipeline for automated analyses of small RNA s in model and nonmodel plants

miRPursuit is a pipeline developed for running end‐to‐end analyses of high‐throughput small RNA ( sRNA ) sequence data in model and nonmodel plants, from raw data to identified and annotated conserved and novel sequences. It consists of a series of UNIX shell scripts, which connect open‐source sRNA...

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Bibliographic Details
Published in:FEBS letters 2017-08, Vol.591 (15), p.2261-2268
Main Authors: Chaves, Inês, Costa, Bruno Vasques, Rodrigues, Andreia S., Bohn, Andreas, Miguel, Célia M.
Format: Article
Language:English
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Summary:miRPursuit is a pipeline developed for running end‐to‐end analyses of high‐throughput small RNA ( sRNA ) sequence data in model and nonmodel plants, from raw data to identified and annotated conserved and novel sequences. It consists of a series of UNIX shell scripts, which connect open‐source sRNA analysis software. The involved parameters can be combined with convenient workflow management by users without advanced computational skills. mi RP ursuit presents several advantages when compared to other tools, including the possibility of processing several sRNA libraries in parallel, thus easily allowing a comparison of the differences in sRNA read accumulation among sRNA libraries. We validate mi RP ursuit by using datasets from a model plant and discuss its performance with the analysis of sRNA s from non‐model species.
ISSN:0014-5793
1873-3468
DOI:10.1002/1873-3468.12746