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- Publisher Website: 10.1093/bioinformatics/btx279
- Scopus: eid_2-s2.0-85044525788
- PMID: 28482046
- WOS: WOS:000408772700021
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Article: rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering
Title | rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering |
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Authors | |
Issue Date | 2017 |
Publisher | Oxford University Press (OUP): Policy B - Oxford Open Option B. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/ |
Citation | Bioinformatics, 2017, v. 33 n. 17, p. 2750-2752 How to Cite? |
Abstract | Motivation: Long read sequencing technologies provide new opportunities to investigate genome structural variations (SVs) more accurately. However, the state-of-the-art SV calling pipelines are computational intensive and the applications of long reads are restricted.
Results: We propose a local region match-based filter (rMFilter) to efficiently nail down chimeric noisy long reads based on short token matches within local genomic regions. rMFilter is able to substantially accelerate long read-based SV calling pipelines without loss of effectiveness. It can be easily integrated into current long read-based pipelines to facilitate SV studies.
Availability and implementation: The C ++ source code of rMFilter is available at https://github.com/hitbc/rMFilter .
Contact: ydwang@hit.edu.cn. |
Persistent Identifier | http://hdl.handle.net/10722/264708 |
ISSN | 2023 Impact Factor: 4.4 2023 SCImago Journal Rankings: 2.574 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Liu, B | - |
dc.contributor.author | Jiang, T | - |
dc.contributor.author | Yiu, SM | - |
dc.contributor.author | Li, JY | - |
dc.contributor.author | Wang, Y | - |
dc.date.accessioned | 2018-10-24T01:49:47Z | - |
dc.date.available | 2018-10-24T01:49:47Z | - |
dc.date.issued | 2017 | - |
dc.identifier.citation | Bioinformatics, 2017, v. 33 n. 17, p. 2750-2752 | - |
dc.identifier.issn | 1367-4803 | - |
dc.identifier.uri | http://hdl.handle.net/10722/264708 | - |
dc.description.abstract | Motivation: Long read sequencing technologies provide new opportunities to investigate genome structural variations (SVs) more accurately. However, the state-of-the-art SV calling pipelines are computational intensive and the applications of long reads are restricted. Results: We propose a local region match-based filter (rMFilter) to efficiently nail down chimeric noisy long reads based on short token matches within local genomic regions. rMFilter is able to substantially accelerate long read-based SV calling pipelines without loss of effectiveness. It can be easily integrated into current long read-based pipelines to facilitate SV studies. Availability and implementation: The C ++ source code of rMFilter is available at https://github.com/hitbc/rMFilter . Contact: ydwang@hit.edu.cn. | - |
dc.language | eng | - |
dc.publisher | Oxford University Press (OUP): Policy B - Oxford Open Option B. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/ | - |
dc.relation.ispartof | Bioinformatics | - |
dc.subject.mesh | Genome, Human | - |
dc.subject.mesh | Genomic Structural Variation | - |
dc.subject.mesh | Genomics | - |
dc.subject.mesh | Humans | - |
dc.subject.mesh | Sequence Analysis, DNA | - |
dc.title | rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering | - |
dc.type | Article | - |
dc.identifier.email | Yiu, SM: smyiu@cs.hku.hk | - |
dc.identifier.authority | Yiu, SM=rp00207 | - |
dc.description.nature | link_to_subscribed_fulltext | - |
dc.identifier.doi | 10.1093/bioinformatics/btx279 | - |
dc.identifier.pmid | 28482046 | - |
dc.identifier.scopus | eid_2-s2.0-85044525788 | - |
dc.identifier.hkuros | 292128 | - |
dc.identifier.volume | 33 | - |
dc.identifier.issue | 17 | - |
dc.identifier.spage | 2750 | - |
dc.identifier.epage | 2752 | - |
dc.identifier.isi | WOS:000408772700021 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 1367-4803 | - |