Evaluation of de novo transcriptome assemblies from RNA-Seq data

BioRxiv : the Preprint Server for Biology
Bo LiColin N Dewey

Abstract

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.

Related Concepts

Ambystoma mexicanum
Genome
RNA
Advice
Evaluation
Research Study
Molecular Assembly/Self Assembly
Species
Study
Transcriptome

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