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Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools
Joint Authors
Porter, Jacob
Tran, Hong
Sun, Ming-an
Xie, Hehuang
Zhang, Liqing
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-04-15
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Natural & Life Sciences (Multidisciplinary)
Biology
Abstract EN
Background.
Large-scale bisulfite treatment and short reads sequencing technology allow comprehensive estimation of methylation states of Cs in the genomes of different tissues, cell types, and developmental stages.
Accurate characterization of DNA methylation is essential for understanding genotype phenotype association, gene and environment interaction, diseases, and cancer.
Aligning bisulfite short reads to a reference genome has been a challenging task.
We compared five bisulfite short read mapping tools, BSMAP, Bismark, BS-Seeker, BiSS, and BRAT-BW, representing two classes of mapping algorithms (hash table and suffix/prefix tries).
We examined their mapping efficiency (i.e., the percentage of reads that can be mapped to the genomes), usability, running time, and effects of changing default parameter settings using both real and simulated reads.
We also investigated how preprocessing data might affect mapping efficiency.
Conclusion.
Among the five programs compared, in terms of mapping efficiency, Bismark performs the best on the real data, followed by BiSS, BSMAP, and finally BRAT-BW and BS-Seeker with very similar performance.
If CPU time is not a constraint, Bismark is a good choice of program for mapping bisulfite treated short reads.
Data quality impacts a great deal mapping efficiency.
Although increasing the number of mismatches allowed can increase mapping efficiency, it not only significantly slows down the program, but also runs the risk of having increased false positives.
Therefore, users should carefully set the related parameters depending on the quality of their sequencing data.
American Psychological Association (APA)
Tran, Hong& Porter, Jacob& Sun, Ming-an& Xie, Hehuang& Zhang, Liqing. 2014. Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools. Advances in Bioinformatics،Vol. 2014, no. 2014, pp.1-11.
https://search.emarefa.net/detail/BIM-474203
Modern Language Association (MLA)
Tran, Hong…[et al.]. Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools. Advances in Bioinformatics No. 2014 (2014), pp.1-11.
https://search.emarefa.net/detail/BIM-474203
American Medical Association (AMA)
Tran, Hong& Porter, Jacob& Sun, Ming-an& Xie, Hehuang& Zhang, Liqing. Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools. Advances in Bioinformatics. 2014. Vol. 2014, no. 2014, pp.1-11.
https://search.emarefa.net/detail/BIM-474203
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-474203