Table of Contents
ISRN Bioinformatics
Volume 2012, Article ID 816402, 9 pages
http://dx.doi.org/10.5402/2012/816402
Research Article

Enhancing De Novo Transcriptome Assembly by Incorporating Multiple Overlap Sizes

1Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
2Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
3Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

Received 20 December 2011; Accepted 9 February 2012

Academic Editors: F. Couto, Q. Dong, H. Hegyi, D. Labudde, C. Ortutay, F. Plewniak, and K. Yura

Copyright © 2012 Chien-Chih Chen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background. The emergence of next-generation sequencing platform gives rise to a new generation of assembly algorithms. Compared with the Sanger sequencing data, the next-generation sequence data present shorter reads, higher coverage depth, and different error profiles. These features bring new challenging issues for de novo transcriptome assembly. Methodology. To explore the influence of these features on assembly algorithms, we studied the relationship between read overlap size, coverage depth, and error rate using simulated data. According to the relationship, we propose a de novo transcriptome assembly procedure, called Euler-mix, and demonstrate its performance on a real transcriptome dataset of mice. The simulation tool and evaluation tool are freely available as open source. Significance. Euler-mix is a straightforward pipeline; it focuses on dealing with the variation of coverage depth of short reads dataset. The experiment result showed that Euler-mix improves the performance of de novo transcriptome assembly.