RSEM-EVAL correctly selects the Trinity assembly of reads originating from a transcript of mouse gene Rpl24 as the best among the default assemblies from Trinity, Oases and SOAPdenovo-Trans. Reads from the mouse strand non-specific single-end data set aligning to transcript 1 of Rpl24 were extracted and assembled by Trinity, Oases and SOAPdenovo-Trans with default parameters. Contigs (filled rectangles) from each assembly were aligned against the true transcript with BLAT to establish their positional identities (blue-yellow fill, with only the segment of a contig from its highest-scoring local alignment shown). RSEM-EVAL was run on each assembly and the likelihood, prior, BIC and total RSEM-EVAL scores were recorded. Although the SOAPdenovo-Trans assembly was smaller (as reflected by the higher prior score), the Trinity assembly had a much higher likelihood score, which is generally the dominant term in the RSEM-EVAL score, and was thus correctly selected as the most accurate assembly. BIC, Bayesian information criterion.