Introduction

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. We 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. Guided by RSEM-EVAL, we assembled the transcriptome of the regenerating axolotl limb; this assembly compares favorably to a previous assembly. A software package implementing our methods, DETONATE, is freely available at http://deweylab.biostat.wisc.edu/detonate.

Publications

  1. Evaluation of de novo transcriptome assemblies from RNA-Seq data.
    Cite this
    Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN, 2014-12-01 - Genome biology

Credits

  1. Bo Li
    Developer

  2. Nathanael Fillmore
    Developer

  3. Yongsheng Bai
    Developer

  4. Mike Collins
    Developer

  5. James A Thomson
    Developer

  6. Ron Stewart
    Developer

  7. Colin N Dewey
    Investigator

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Summary
AccessionBT007054
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByColin N Dewey