PT - JOURNAL ARTICLE AU - Colin Farrell AU - Michael Thompson AU - Anela Tosevska AU - Adewale Oyetunde AU - Matteo Pellegrini TI - BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform AID - 10.1101/2020.10.06.328559 DP - 2021 Jan 01 TA - bioRxiv PG - 2020.10.06.328559 4099 - http://biorxiv.org/content/early/2021/02/05/2020.10.06.328559.short 4100 - http://biorxiv.org/content/early/2021/02/05/2020.10.06.328559.full 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.