RT Journal Article SR Electronic T1 Evaluation of de novo transcriptome assemblies from RNA-Seq data JF bioRxiv FD Cold Spring Harbor Laboratory SP 006338 DO 10.1101/006338 A1 Bo Li A1 Nathanael Fillmore A1 Yongsheng Bai A1 Mike Collins A1 James A. Thomson A1 Ron Stewart A1 Colin N. Dewey YR 2014 UL http://biorxiv.org/content/early/2014/06/13/006338.abstract 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.