BS Seeker: precise mapping for bisulfite sequencing

Background: Bisulfite sequencing using next generation sequencers yields genome-wide measurements of DNA methylation at single nucleotide resolution. Traditional aligners are not designed for mapping bisulfite-treated reads, where the unmethylated Cs are converted to Ts. We have developed BS Seeker, an approach that converts the genome to a three-letter alphabet and uses Bowtie to align bisulfite-treated reads to a reference genome. It uses sequence tags to reduce mapping ambiguity. Post-processing of the alignments removes non-unique and low-quality mappings. Results: We tested our aligner on synthetic data, a bisulfite-converted Arabidopsis library, and human libraries generated from two different experimental protocols. We evaluated the performance of our approach and compared it to other bisulfite aligners. The results demonstrate that among the aligners tested, BS Seeker is more versatile and faster. When mapping to the human genome, BS Seeker generates alignments significantly f...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Pao-Yang Chen, Shawn Cokus, Matteo Pellegrini
• Keywords: Bisulfite-treated Reads, BMCBI 2010, DNA Methylation, Unmethylated Cs