rnaQUAST: a quality assessment tool for de novo transcriptome assemblies

Ability to generate large RNA-Seq datasets created a demand for both de novo and reference-based transcriptome assemblers. However, while many transcriptome assemblers are now available, there is still no unified quality assessment tool for RNA-Seq assemblies. We present rnaQUAST—a tool for evaluati...

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Published inBioinformatics (Oxford, England) Vol. 32; no. 14; pp. 2210 - 2212
Main Authors Bushmanova, Elena, Antipov, Dmitry, Lapidus, Alla, Suvorov, Vladimir, Prjibelski, Andrey D.
Format Journal Article
LanguageEnglish
Published England 15.07.2016
Subjects
Computational Biology - methods
Sequence Analysis, RNA
Software
Transcriptome
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Summary:Ability to generate large RNA-Seq datasets created a demand for both de novo and reference-based transcriptome assemblers. However, while many transcriptome assemblers are now available, there is still no unified quality assessment tool for RNA-Seq assemblies. We present rnaQUAST—a tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. rnaQUAST calculates various metrics that demonstrate completeness and correctness levels of the assembled transcripts, and outputs them in a user-friendly report. Availability and Implementation: rnaQUAST is implemented in Python and is freely available at http://bioinf.spbau.ru/en/rnaquast. Contact:  ap@bioinf.spbau.ru Supplementary information:  Supplementary data are available at Bioinformatics online.
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ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btw218