Table of Contents
ISRN Bioinformatics
Volume 2012 (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.

Supplementary Material

Figures S1~S4 show the relationship between optimum k's and coverage depth for four transcriptome sequences in different error rate.

Table S1 shows the results on the simulated data executed by Euler-SR with k from 19 to 27, and by Euler-mix using Euler-SR as the underlying algorithm. Table S2 shows the results on the simulated data executed by ABySS with k from 19 to 35, and by Euler-mix using ABySS as the underlying algorithm. Table S3 shows the results on the simulated data executed by Edena with k from 19 to 35, and by Euler-mix using Edena as the underlying algorithm.

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