Cloud-BS: A MapReduce-based bisulfite sequencing aligner on cloud
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Choi, Joungmin | - |
dc.contributor.author | Park, Yoonjae | - |
dc.contributor.author | Kim, Sun | - |
dc.contributor.author | Chae, Heejoon | - |
dc.date.available | 2021-02-22T07:46:20Z | - |
dc.date.issued | 2018-12 | - |
dc.identifier.issn | 0219-7200 | - |
dc.identifier.issn | 1757-6334 | - |
dc.identifier.uri | https://scholarworks.sookmyung.ac.kr/handle/2020.sw.sookmyung/4146 | - |
dc.description.abstract | In recent years, there have been many studies utilizing DNA methylome data to answer fundamental biological questions. Bisulfite sequencing (BS-seq) has enabled measurement of a genome-wide absolute level of DNA methylation at single-nucleotide resolution. However, due to the ambiguity introduced by bisulfite-treatment, the aligning process especially in large-scale epigenetic research is still considered a huge burden. We present Cloud-BS, an efficient BS-seq aligner designed for parallel execution on a distributed environment. Utilizing Apache Hadoop framework, Cloud-BS splits sequencing reads into multiple blocks and transfers them to distributed nodes. By designing each aligning procedure into separate map and reducing tasks while an internal key-value structure is optimized based on the MapReduce programming model, the algorithm significantly improves alignment performance without sacrificing mapping accuracy. In addition, Cloud-BS minimizes the innate burden of configuring a distributed environment by providing a pre-configured cloud image. Cloud-BS shows significantly improved bisulfite alignment performance compared to other existing BS-seq aligners. We believe our algorithm facilitates large-scale methylome data analysis. The algorithm is freely available at https://paryoja.github.io/Cloud-BS/. | - |
dc.language | 영어 | - |
dc.language.iso | ENG | - |
dc.publisher | IMPERIAL COLLEGE PRESS | - |
dc.title | Cloud-BS: A MapReduce-based bisulfite sequencing aligner on cloud | - |
dc.type | Article | - |
dc.publisher.location | 영국 | - |
dc.identifier.doi | 10.1142/S0219720018400280 | - |
dc.identifier.scopusid | 2-s2.0-85058816434 | - |
dc.identifier.wosid | 000455392200007 | - |
dc.identifier.bibliographicCitation | JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, v.16, no.6 | - |
dc.citation.title | JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY | - |
dc.citation.volume | 16 | - |
dc.citation.number | 6 | - |
dc.type.docType | Article; Proceedings Paper | - |
dc.description.isOpenAccess | N | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Biochemistry & Molecular Biology | - |
dc.relation.journalResearchArea | Computer Science | - |
dc.relation.journalResearchArea | Mathematical & Computational Biology | - |
dc.relation.journalWebOfScienceCategory | Biochemical Research Methods | - |
dc.relation.journalWebOfScienceCategory | Computer Science, Interdisciplinary Applications | - |
dc.relation.journalWebOfScienceCategory | Mathematical & Computational Biology | - |
dc.subject.keywordPlus | DNA METHYLATION | - |
dc.subject.keywordPlus | PIPELINE | - |
dc.subject.keywordPlus | ALIGNMENT | - |
dc.subject.keywordPlus | SOFTWARE | - |
dc.subject.keywordPlus | CANCER | - |
dc.subject.keywordAuthor | Bisulfite sequencing | - |
dc.subject.keywordAuthor | aligner | - |
dc.subject.keywordAuthor | distributed | - |
dc.subject.keywordAuthor | MapReduce | - |
dc.subject.keywordAuthor | cloud | - |
dc.identifier.url | https://www.worldscientific.com/doi/abs/10.1142/S0219720018400280 | - |
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