BiSulfite Bolt: A bisulfite sequencing analysis platform
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Abstract
Background
Bisulfite sequencing is commonly used to measure DNA methylation. Processing bisulfite sequencing data is often challenging owing 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.
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Now published in GigaScience doi: 10.1093/gigascience/giab033
Colin Farrell 1Department of Human Genetics, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Colin FarrellMichael Thompson 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnela Tosevska 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdewale Oyetunde 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author …
Now published in GigaScience doi: 10.1093/gigascience/giab033
Colin Farrell 1Department of Human Genetics, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Colin FarrellMichael Thompson 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnela Tosevska 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdewale Oyetunde 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMatteo Pellegrini 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: matteop@mcdb.ucla.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab033 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102730 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102731
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