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Open Access Highly Accessed Research article

Assessing De Novo transcriptome assembly metrics for consistency and utility

Shawn T O’Neil12 and Scott J Emrich2*

Author Affiliations

1 Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97333, USA

2 Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA

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BMC Genomics 2013, 14:465  doi:10.1186/1471-2164-14-465

Published: 9 July 2013

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 contig coverage and length, though they became consistent when singletons were included in the analysis. We found several annotation-based metrics to be consistent and informative, including contig reciprocal best hit count and contig unique annotation count. Finally, we evaluated a number of novel metrics such as reverse annotation count, contig collapse factor, and the ortholog hit ratio, discovering that each assess assembly quality in unique ways.

Conclusions

Although much attention has been given to transcriptome assembly, little research has focused on determining how best to evaluate assemblies, particularly in light of the variety of options available for read length and sequencing depth. Our results provide an important review of these metrics and give researchers tools to produce the highest quality transcriptome assemblies.