Figure 1.

Genome-wide hairpin bisulfite sequence generation and processing. The flow chart begins with double stranded genomic DNA ligated to hairpin adapter. Hairpin bisulfite PCR products are sequenced from both ends. HBS-tools accept these pair-end hairpin-BS-Seq reads to recover the original (pre-bisulfite converted) sequences. The recovered sequences are aligned with the reference genome. Methylation calls are obtained based on the sequence alignment between raw sequence reads and corresponding genome sequences.