Ability to generate large RNA-Seq data sets 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. Keywords: RNA-Seq, transcriptome assembly, quality assessment. Contact: ap@bioinf.spbau.ru Supplementary material: To be posted online.