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BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Soe, Seokjun | - |
dc.contributor.author | Park, Yoonjae | - |
dc.contributor.author | Chae, Heejoon | - |
dc.date.accessioned | 2019-03-12T01:36:08Z | - |
dc.date.available | 2019-03-12T10:37:46Z | - |
dc.date.issued | 2018-12-10 | - |
dc.identifier.citation | BMC Bioinformatics, 19(1):472 | ko_KR |
dc.identifier.issn | 1471-2105 | - |
dc.identifier.uri | https://hdl.handle.net/10371/146970 | - |
dc.description.abstract | Background
Bisulfite sequencing is one of the major high-resolution DNA methylation measurement method. Due to the selective nucleotide conversion on unmethylated cytosines after treatment with sodium bisulfite, processing bisulfite-treated sequencing reads requires additional steps which need high computational demands. However, a dearth of efficient aligner that is designed for bisulfite-treated sequencing becomes a bottleneck of large-scale DNA methylome analyses. Results In this study, we present a highly scalable, efficient, and load-balanced bisulfite aligner, BiSpark, which is designed for processing large volumes of bisulfite sequencing data. We implemented the BiSpark algorithm over the Apache Spark, a memory optimized distributed data processing framework, to achieve the maximum data parallel efficiency. The BiSpark algorithm is designed to support redistribution of imbalanced data to minimize delays on large-scale distributed environment. Conclusions Experimental results on methylome datasets show that BiSpark significantly outperforms other state-of-the-art bisulfite sequencing aligners in terms of alignment speed and scalability with respect to dataset size and a number of computing nodes while providing highly consistent and comparable mapping results. Availability The implementation of BiSpark software package and source code is available at https://github.com/bhi-kimlab/BiSpark/ . | ko_KR |
dc.description.sponsorship | This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP; Ministry of Science, ICT & Future Planning) (No. 2017R1C1B5018165), supported by Basic Science Research Program through the NRF funded by the Ministry of Education
(NRF-2016R1D1A1A02937186), supported by a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number : HI15C3224), and also supported by the Sookmyung Womens University Research Grants (1-1703-2032). | ko_KR |
dc.language.iso | en | ko_KR |
dc.publisher | BioMed Central | ko_KR |
dc.subject | DNA methylation | ko_KR |
dc.subject | Bisulfite sequencing | ko_KR |
dc.subject | Alignment | ko_KR |
dc.subject | Apache Spark | ko_KR |
dc.title | BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data | ko_KR |
dc.type | Article | ko_KR |
dc.contributor.AlternativeAuthor | 소석준 | - |
dc.contributor.AlternativeAuthor | 박윤재 | - |
dc.contributor.AlternativeAuthor | 채희준 | - |
dc.identifier.doi | 10.1186/s12859-018-2498-2 | - |
dc.language.rfc3066 | en | - |
dc.rights.holder | The Author(s) | - |
dc.date.updated | 2018-12-16T04:14:33Z | - |
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