Enhancing De Novo Transcriptome Assembly by Incorporating Multiple Overlap Sizes
Joint Authors
Ho, Jan-Ming
Chen, Chuen-Liang
Lin, Wen-Dar
Chang, Yu-Jung
Chen, Chien-Chih
Source
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-04-23
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Chen, Chien-Chih& Lin, Wen-Dar& Chang, Yu-Jung& Chen, Chuen-Liang& Ho, Jan-Ming. 2012. Enhancing De Novo Transcriptome Assembly by Incorporating Multiple Overlap Sizes. ISRN Bioinformatics،Vol. 2012, no. 2012, pp.1-9.
https://search.emarefa.net/detail/BIM-500399
Modern Language Association (MLA)
Chen, Chien-Chih…[et al.]. Enhancing De Novo Transcriptome Assembly by Incorporating Multiple Overlap Sizes. ISRN Bioinformatics No. 2012 (2012), pp.1-9.
https://search.emarefa.net/detail/BIM-500399
American Medical Association (AMA)
Chen, Chien-Chih& Lin, Wen-Dar& Chang, Yu-Jung& Chen, Chuen-Liang& Ho, Jan-Ming. Enhancing De Novo Transcriptome Assembly by Incorporating Multiple Overlap Sizes. ISRN Bioinformatics. 2012. Vol. 2012, no. 2012, pp.1-9.
https://search.emarefa.net/detail/BIM-500399
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-500399