Table of Contents
Computational Biology Journal
Volume 2014, Article ID 961823, 4 pages
http://dx.doi.org/10.1155/2014/961823
Research Article

A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs

1Department of Computer Science, Virginia Tech, Blacksburg, VA 24060, USA
2Fralin Life Science Institute, Virginia Tech, Blacksburg, VA 24060, USA

Received 27 January 2014; Revised 18 April 2014; Accepted 4 May 2014; Published 28 May 2014

Academic Editor: Giancarlo Mauri

Copyright © 2014 Mingming Liu 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

With the rapid development of high throughput sequencing technologies, new transcriptomes can be sequenced for little cost with high coverage. Sequence assembly approaches have been modified to meet the requirements for de novo transcriptomes, which have complications not found in traditional genome assemblies such as variation in coverage for each candidate mRNA and alternative splicing. As a consequence, de novo assembly strategies tend to generate a large number of redundant contigs due to sequence variations, which adversely affects downstream analysis and experiments. In this work we proposed TransPS, a transcriptome post-scaffolding method, to generate high quality, nonredundant de novo transcriptomes. TransPS shows promising results on the test transcriptome datasets, where redundancy is greatly reduced by more than 50% and, at the same time, coverage is improved considerably. The web server and source code are available.