A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing

Xuefeng Wang; Xiaoqing Yu; Wei Zhu; W Richard McCombie; Eric Antoniou; R Scott Powers; Nicholas O Davidson; Ellen Li; Jennie Williams

doi:10.1093/bioinformatics/btv089

A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing

Bioinformatics. 2015 Jun 15;31(12):2040-2. doi: 10.1093/bioinformatics/btv089. Epub 2015 Feb 13.

Authors

Xuefeng Wang¹, Xiaoqing Yu², Wei Zhu², W Richard McCombie², Eric Antoniou², R Scott Powers³, Nicholas O Davidson², Ellen Li², Jennie Williams²

Affiliations

¹ Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
² Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
³ Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.

Abstract

Currently available bisulfite sequencing tools frequently suffer from low mapping rates and low methylation calls, especially for data generated from the Illumina sequencer, NextSeq. Here, we introduce a sequential trimming-and-retrieving alignment approach for investigating DNA methylation patterns, which significantly improves the number of mapped reads and covered CpG sites. The method is implemented in an automated analysis toolkit for processing bisulfite sequencing reads.

Availability and implementation: http://mysbfiles.stonybrook.edu/~xuefenwang/software.html and https://github.com/xfwang/BStools.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

DNA Methylation*
High-Throughput Nucleotide Sequencing / methods*
Humans
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Software*
Sulfites / chemistry*

Substances

Sulfites
hydrogen sulfite

Abstract

Publication types

MeSH terms

Substances

Grants and funding