Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data
UMass Chan Affiliations
Program in Bioinformatics and Integrative BiologyDocument Type
Journal ArticlePublication Date
2015-12-01Keywords
DNA methylationWGBS analysis step evaluation
WGBS mapping software
read quality trimming
whole genome bisulfite sequencing
Bioinformatics
Computational Biology
Genomics
Metadata
Show full item recordAbstract
Cytosine methylation regulates many biological processes such as gene expression, chromatin structure and chromosome stability. The whole genome bisulfite sequencing (WGBS) technique measures the methylation level at each cytosine throughout the genome. There are an increasing number of publicly available pipelines for analyzing WGBS data, reflecting many choices of read mapping algorithms as well as preprocessing and postprocessing methods. We simulated single-end and paired-end reads based on three experimental data sets, and comprehensively evaluated 192 combinations of three preprocessing, five postprocessing and five widely used read mapping algorithms. We also compared paired-end data with single-end data at the same sequencing depth for performance of read mapping and methylation level estimation. Bismark and LAST were the most robust mapping algorithms. We found that Mott trimming and quality filtering individually improved the performance of both read mapping and methylation level estimation, but combining them did not lead to further improvement. Furthermore, we confirmed that paired-end sequencing reduced error rate and enhanced sensitivity for both read mapping and methylation level estimation, especially for short reads and in repetitive regions of the human genome.Source
Brief Bioinform. 2015 Dec 1. pii: bbv103. Link to article on publisher's siteDOI
10.1093/bib/bbv103Permanent Link to this Item
http://hdl.handle.net/20.500.14038/25927PubMed ID
26628557Related Resources
Link to Article in PubMedae974a485f413a2113503eed53cd6c53
10.1093/bib/bbv103