RT Journal Article SR Electronic T1 BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.10.06.328559 DO 10.1101/2020.10.06.328559 A1 Farrell, Colin A1 Thompson, Michael A1 Tosevska, Anela A1 Oyetunde, Adewale A1 Pellegrini, Matteo YR 2021 UL http://biorxiv.org/content/early/2021/02/05/2020.10.06.328559.abstract AB Background Bisulfite sequencing is commonly employed to measure DNA methylation. Processing bisulfite sequencing data is often challenging due to the computational demands of mapping a low complexity, asymmetrical library and the lack of a unified processing toolset to produce an analysis ready methylation matrix from read alignments. To address these shortcomings, we have developed BiSulfite Bolt (BSBolt); a fast and scalable bisulfite sequencing analysis platform. BSBolt performs a pre-alignment sequencing read assessment step to improve efficiency when handling asymmetrical bisulfite sequencing libraries.Findings We evaluated BSBolt against simulated and real bisulfite sequencing libraries. We found that BSBolt provides accurate and fast bisulfite sequencing alignments and methylation calls. We also compared BSBolt to several existing bisulfite alignment tools and found BSBolt outperforms Bismark, BSSeeker2, BISCUIT, and BWA-Meth based on alignment accuracy and methylation calling accuracy.Conclusion BSBolt offers streamlined processing of bisulfite sequencing data through an integrated toolset that offers support for simulation, alignment, methylation calling, and data aggregation. BSBolt is implemented as a python package and command line utility for flexibility when building informatics pipelines. BSBolt is available at https://github.com/NuttyLogic/BSBolt under an MIT license.Competing Interest StatementThe authors have declared no competing interest.