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Nucleic Acids Res. 2012 May;40(10):e79. doi: 10.1093/nar/gks150. Epub 2012 Feb 16.

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

Author information

1
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand.

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.

PMID:
22344695
PMCID:
PMC3378906
DOI:
10.1093/nar/gks150
[Indexed for MEDLINE]
Free PMC Article

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