Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data

• DOI: 10.1093/bib/bbv103
• Publication Date: 2015-12-02T01:38:31Z
• Authors: Junko Tsuji; Zhiping Weng
• Keywords: Bisulfite sequencing

Cytosine methylation regulates many biological processes such as gene expression, chromatin structure and chromosome stability. The whole genome bisulfite sequencing (WGBS) technique measures the level at each cytosine throughout genome. There are an increasing number of publicly available pipelines for analyzing WGBS data, reflecting choices read mapping algorithms well preprocessing postprocessing methods. We simulated single-end paired-end reads based on three experimental data sets, comprehensively evaluated 192 combinations preprocessing, five widely used algorithms. also compared with same depth performance estimation. Bismark LAST were most robust found that Mott trimming quality filtering individually improved both estimation, but combining them did not lead to further improvement. Furthermore, we confirmed reduced error rate enhanced sensitivity especially short in repetitive regions human