Comparison of alignment software for genome-wide bisulphite sequence data.

Nucleic Acids Research
Aniruddha ChatterjeeIan M Morison

Abstract

Recent advances in next generation sequencing (NGS) technology now provide the opportunity to rapidly interrogate the methylation status of the genome. However, there are challenges in handling and interpretation of the methylation sequence data because of its large volume and the consequences of bisulphite modification. We sequenced reduced representation human genomes on the Illumina platform and efficiently mapped and visualized the data with different pipelines and software packages. We examined three pipelines for aligning bisulphite converted sequencing reads and compared their performance. We also comment on pre-processing and quality control of Illumina data. This comparison highlights differences in methods for NGS data processing and provides guidance to advance sequence-based methylation data analysis for molecular biologists.

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Methods Mentioned

BETA
PCR
RRBS
Illumina sequencing
methylation

Software Mentioned

meth
R
CokusAlign
BSMAP
Programme Aligner
MacOS X
mkrrgenome
SeqMonk
Bismark
RMAPBS

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