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- Publisher Website: 10.1145/3388440.3412457
- Scopus: eid_2-s2.0-85096991599
- WOS: WOS:000936196100027
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Conference Paper: Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads
Title | Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads |
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Authors | |
Issue Date | 2020 |
Publisher | Association for Computing Machinery. |
Citation | Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Virtual Conference, Atlanta, GA, USA, 21-24 September 2020, Article No. 15:1-7 How to Cite? |
Abstract | Translocation is an important class of structural variants known to be associated with cancer formation and treatment. The recent development in single-molecule sequencing technologies that produce long reads has promised an advance in detecting translocations accurately. However, existing tools struggled with the high base error-rate of the long reads. Figuring out the correct translocation breakpoints is especially challenging due to suboptimally aligned reads. To address the problem, we developed Translocator, a robust and accurate translocation detection method that implements an effective realignment algorithm to recover the correct alignments. For benchmarking, we analyzed using NA12878 long reads against a modified GRCh38 reference genome embedded with translocations at known locations. Our results show that Translocator significantly outperformed other state-of-the-art methods, including Sniffles and PBSV. On Oxford Nanopore data, the recall improved from 48.2% to 87.5% and the precision from 88.7% to 92.7%. Translocator is available open-source at https://github.com/HKU-BAL/Translocator. |
Persistent Identifier | http://hdl.handle.net/10722/294304 |
ISBN | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Wu, Y | - |
dc.contributor.author | Luo, R | - |
dc.contributor.author | Lam, TW | - |
dc.contributor.author | Ting, HF | - |
dc.contributor.author | Wang, J | - |
dc.date.accessioned | 2020-11-23T08:29:28Z | - |
dc.date.available | 2020-11-23T08:29:28Z | - |
dc.date.issued | 2020 | - |
dc.identifier.citation | Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Virtual Conference, Atlanta, GA, USA, 21-24 September 2020, Article No. 15:1-7 | - |
dc.identifier.isbn | 9781450379649 | - |
dc.identifier.uri | http://hdl.handle.net/10722/294304 | - |
dc.description.abstract | Translocation is an important class of structural variants known to be associated with cancer formation and treatment. The recent development in single-molecule sequencing technologies that produce long reads has promised an advance in detecting translocations accurately. However, existing tools struggled with the high base error-rate of the long reads. Figuring out the correct translocation breakpoints is especially challenging due to suboptimally aligned reads. To address the problem, we developed Translocator, a robust and accurate translocation detection method that implements an effective realignment algorithm to recover the correct alignments. For benchmarking, we analyzed using NA12878 long reads against a modified GRCh38 reference genome embedded with translocations at known locations. Our results show that Translocator significantly outperformed other state-of-the-art methods, including Sniffles and PBSV. On Oxford Nanopore data, the recall improved from 48.2% to 87.5% and the precision from 88.7% to 92.7%. Translocator is available open-source at https://github.com/HKU-BAL/Translocator. | - |
dc.language | eng | - |
dc.publisher | Association for Computing Machinery. | - |
dc.relation.ispartof | The 11th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) Proceedings | - |
dc.rights | The 11th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) Proceedings. Copyright © Association for Computing Machinery. | - |
dc.title | Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads | - |
dc.type | Conference_Paper | - |
dc.identifier.email | Luo, R: rbluo@cs.hku.hk | - |
dc.identifier.email | Lam, TW: twlam@cs.hku.hk | - |
dc.identifier.email | Ting, HF: hfting@cs.hku.hk | - |
dc.identifier.authority | Luo, R=rp02360 | - |
dc.identifier.authority | Lam, TW=rp00135 | - |
dc.identifier.authority | Ting, HF=rp00177 | - |
dc.identifier.doi | 10.1145/3388440.3412457 | - |
dc.identifier.scopus | eid_2-s2.0-85096991599 | - |
dc.identifier.hkuros | 318778 | - |
dc.identifier.spage | article No. 15:1 | - |
dc.identifier.epage | article No. 15:7 | - |
dc.identifier.isi | WOS:000936196100027 | - |
dc.publisher.place | New York, NY | - |