BS-Seeker2

BS-Seeker2 is a bioinformatics software tool designed to aid in mapping bisulfite sequencing data and generating DNA methylomes. Bisulfite sequencing is an effective approach for studying genome-wide DNA methylation at base resolution. Libraries such as whole genome bisulfite sequencing (WGBS) and reduced represented bisulfite sequencing (RRBS) are widely used for generating DNA methylomes and demand efficient and versatile tools for aligning bisulfite sequencing data.
BS-Seeker2 is an updated version of BS Seeker, and it works by improving mappability over existing aligners by using local alignment. It can also map reads from RRBS library by building special indexes with improved efficiency and accuracy, which allows for efficient and accurate mapping of reads from the library. Moreover, BS-Seeker2 provides an additional function for filtering out reads with incomplete bisulfite conversion, which is helpful in minimizing the overestimation of DNA methylation levels.
BS-Seeker2 offers a comprehensive output of CGmap and ATCGmap file formats for full representations of DNA methylomes as part of the outputs of the BS-Seeker2 pipeline together with BAM and WIG files. The software tool has been evaluated and shown to work efficiently and accurately for WGBS and RRBS data.