PT - JOURNAL ARTICLE AU - Li, Bo AU - Fillmore, Nathanael AU - Bai, Yongsheng AU - Collins, Mike AU - Thomson, James A. AU - Stewart, Ron AU - Dewey, Colin N. TI - Evaluation of <em>de novo</em> transcriptome assemblies from RNA-Seq data AID - 10.1101/006338 DP - 2014 Jan 01 TA - bioRxiv PG - 006338 4099 - http://biorxiv.org/content/early/2014/06/13/006338.short 4100 - http://biorxiv.org/content/early/2014/06/13/006338.full AB - De novo RNA-Seq assembly facilitates the study of transcriptomes for species without sequenced genomes, but it is challenging to select the most accurate assembly in this context. To address this challenge, we developed a model-based score, RSEM-EVAL, for evaluating assemblies when the ground truth is unknown. Our experiments show that RSEM-EVAL correctly reflects assembly accuracy, as measured by REF-EVAL, a refined set of ground-truth-based scores that we also developed. With the guidance of RSEM-EVAL, we assembled the transcriptome of the regenerating axolotl limb; this assembly compares favorably to a previous assembly.