Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

Abstract

Summary: A combination of bisulfite treatment of DNA and high-throughput sequencing (BS-Seq) can capture a snapshot of a cell's epigenomic state by revealing its genome-wide cytosine methylation at single base resolution. Bismark is a flexible tool for the time-efficient analysis of BS-Seq data which performs both read mapping and methylation calling in a single convenient step. Its output discriminates between cytosines in CpG, CHG and CHH context and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed.

Availability and implementation: Bismark is released under the GNU GPLv3+ licence. The source code is freely available from www.bioinformatics.bbsrc.ac.uk/projects/bismark/.

Fig. 1.

Bismark's approach to bisulfite mapping and methylation calling. (A) Reads from a BS-Seq experiment are converted into a C-to-T and a G-to-A version and are then aligned to equivalently converted versions of the reference genome. A unique best alignment is then determined from the four parallel alignment processes [in this example, the best alignment has no mismatches and comes from thread (1)]. (B) The methylation state of positions involving cytosines is determined by comparing the read sequence with the corresponding genomic sequence. Depending on the strand a read mapped against this can involve looking for C-to-T (as shown here) or G-to-A substitutions.