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Bioinformatics. 2012 Feb 1;28(3):428-9. doi: 10.1093/bioinformatics/btr660. Epub 2011 Dec 6.

B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data.

Author information

1
Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany. b.kreck@ikmb.uni-kiel.de

Abstract

SUMMARY:

Bisulfite sequencing, a combination of bisulfite treatment and high-throughput sequencing, has proved to be a valuable method for measuring DNA methylation at single base resolution. Here, we present B-SOLANA, an approach for the analysis of two-base encoding (colorspace) bisulfite sequencing data on the SOLiD platform of Life Technologies. It includes the alignment of bisulfite sequences and the determination of methylation levels in CpG as well as non-CpG sequence contexts. B-SOLANA enables a fast and accurate analysis of large raw sequence datasets.

AVAILABILITY AND IMPLEMENTATION:

The source code, released under the GNU GPLv3 licence, is freely available at http://code.google.com/p/bsolana/.

CONTACT:

b.kreck@ikmb.uni-kiel.de

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
22155865
PMCID:
PMC3268236
DOI:
10.1093/bioinformatics/btr660
[Indexed for MEDLINE]
Free PMC Article

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