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

Davide Campagna, Andrea Telatin, Claudio Forcato, Nicola Vitulo, Giorgio Valle

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

Bioinformatics (Oxford, England) 2013 Jan 15

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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. pass@cribi.unipd.it Supplementary data are available at Bioinformatics online.

Citation

Davide Campagna, Andrea Telatin, Claudio Forcato, Nicola Vitulo, Giorgio Valle. PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. Bioinformatics (Oxford, England). 2013 Jan 15;29(2):268-70