Assessing De Novo transcriptome assembly metrics for consistency and utility.

ABSTRACT:

Background

Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality.

Results

We simulated sequencing transcripts of Drosophila melanogaster. By assembling these simulated reads using both a "perfect" and a modern transcriptome assembler while varying read length and sequencing depth, we evaluated quality metrics to determine whether they 1) revealed perfect assemblies to be of higher quality, and 2) revealed perfect assemblies to be more complete as data quantity increased.Several commonly used metrics were not consistent with these expectations, including average co

SUBMITTER: O'Neil ST 

PROVIDER: S-EPMC3733778 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature