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Updated: May 16, 2026
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
Published on: February 24, 2015
PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads
Davide Campagna1, Andrea Telatin, Claudio Forcato
1CRIBI Biotechnology Centre, Università di Padova, 35131 Padova, Italy.
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.
