Table of Contents
Computational Biology Journal
Volume 2014, Article ID 961823, 4 pages
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.

Supplementary Material

In the supplementary file, we described the align-layout-consensus strategy used in the paper in detail. In the consensus stage, a scaffolding algorithm is used to join contigs that match to the same reference sequence. Two cases are considered in the scaffolding algorithm: overlapping and nonoverlapping, depending on whether the matching intervals of two query contigs against the same reference sequence are overlapped or not. The pseudocode of the scaffolding algorithm is also provided.

  1. Supplementary Material