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, a team led by researchers at the University of Wisconsin, Madison developed a model-based score, RSEM-EVAL, for evaluating assemblies when the ground truth is unknown. They show that RSEM-EVAL correctly reflects assembly accuracy, as measured by REF-EVAL, a refined set of ground-truth-based scores that the team also developed. Guided by RSEM-EVAL, the researchers assembled the transcriptome of the regenerating axolotl limb; this assembly compares favorably to a previous assembly.
Availability – A software package implementing our methods, DETONATE, is freely available at http://deweylab.biostat.wisc.edu/detonate