miRPursuit—a pipeline for automated analyses of small RNAs in model and nonmodel plants

Inês Chaves, Bruno Vasques Costa, Andreia S. Rodrigues, Andreas Bohn, Célia M. Miguel

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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. miRPursuit 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 miRPursuit by using datasets from a model plant and discuss its performance with the analysis of sRNAs from non-model species.

Original languageEnglish
Pages (from-to)2261-2268
Number of pages8
JournalFEBS Letters
Volume591
Issue number15
DOIs
Publication statusPublished - 1 Aug 2017

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Pipelines
RNA
Libraries
Workflow
Conserved Sequence
UNIX
Software
Throughput
Processing

Keywords

  • microRNA
  • NGS data analysis
  • small noncoding RNA
  • tasiRNA

Cite this

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miRPursuit—a pipeline for automated analyses of small RNAs in model and nonmodel plants. / Chaves, Inês; Costa, Bruno Vasques; Rodrigues, Andreia S.; Bohn, Andreas; Miguel, Célia M.

In: FEBS Letters, Vol. 591, No. 15, 01.08.2017, p. 2261-2268.

Research output: Contribution to journalArticle

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