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Bioinformatics. 2013 Jan 15;29(2):268-70. doi: 10.1093/bioinformatics/bts675. Epub 2012 Nov 17.

PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.

Author information

1
CRIBI Biotechnology Centre, Università di Padova, 35131 Padova, Italy.

Abstract

SUMMARY:

The sequencing of bisulfite-treated DNA (Bi-Seq) is becoming a gold standard for methylation studies. The mapping of Bi-Seq reads is complex and requires special alignment algorithms. This problem is particularly relevant for SOLiD color space, where the bisulfite conversion C/T changes two adjacent colors into 16 possible combinations. Here, we present an algorithm that efficiently aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying methylation-caller program creates a genomic view of methylated and unmethylated Cs on both DNA strands.

AVAILABILITY AND IMPLEMENTATION:

The algorithm has been implemented as an option of the program PASS, freely available at http://pass.cribi.unipd.it.

CONTACT:

pass@cribi.unipd.it

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
23162053
DOI:
10.1093/bioinformatics/bts675
[Indexed for MEDLINE]

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