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BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform

View ORCID ProfileColin Farrell, Michael Thompson, Anela Tosevska, Adewale Oyetunde, Matteo Pellegrini
doi: https://doi.org/10.1101/2020.10.06.328559
Colin Farrell
1Department of Human Genetics, University of California, Los Angeles, CA, USA
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Michael Thompson
2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
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Anela Tosevska
2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
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Adewale Oyetunde
2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
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Matteo Pellegrini
2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
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  • For correspondence: matteop@mcdb.ucla.edu
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Abstract

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 Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/NuttyLogic/BSBolt

  • https://github.com/NuttyLogic/BSBoltManuscript

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 05, 2021.
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BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform
Colin Farrell, Michael Thompson, Anela Tosevska, Adewale Oyetunde, Matteo Pellegrini
bioRxiv 2020.10.06.328559; doi: https://doi.org/10.1101/2020.10.06.328559
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BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform
Colin Farrell, Michael Thompson, Anela Tosevska, Adewale Oyetunde, Matteo Pellegrini
bioRxiv 2020.10.06.328559; doi: https://doi.org/10.1101/2020.10.06.328559

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