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BiSulfite Bolt: A bisulfite sequencing analysis platform
- Source :
- GigaScience, vol 10, iss 5, GigaScience
- Publication Year :
- 2021
- Publisher :
- eScholarship, University of California, 2021.
-
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.
- Subjects :
- Computer science
AcademicSubjects/SCI02254
Bisulfite sequencing
Health Informatics
computer.software_genre
03 medical and health sciences
Technical Note
Sulfites
MIT License
030304 developmental biology
computer.programming_language
0303 health sciences
030305 genetics & heredity
High-Throughput Nucleotide Sequencing
Methylation
Sequence Analysis, DNA
DNA
Python (programming language)
DNA Methylation
Computer Science Applications
Bisulfite
Networking and Information Technology R&D
DNA methylation
Scalability
AcademicSubjects/SCI00960
Data mining
Generic health relevance
computer
Sequence Alignment
Sequence Analysis
Software
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- GigaScience, vol 10, iss 5, GigaScience
- Accession number :
- edsair.doi.dedup.....e62bbfebee642e1ef35fe5a538c42fb0