rnaQUAST: a quality assessment tool for de novo transcriptome assemblies

  • Bioinformatics. 2016 Jul 15;32(14):2210-2. doi: 10.1093/bioinformatics/btw218.
Elena Bushmanova  1 ,  Dmitry Antipov  1 ,  Alla Lapidus  2 ,  Vladimir Suvorov  3 ,  Andrey D Prjibelski  2
Affiliations
  • 1. Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
  • 2. Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
  • 3. Research and Development Department, EMC, St. Petersburg, Russia.
PMID: 27153654 DOI: 10.1093/bioinformatics/btw218
Abstract

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: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.