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- Publisher Website: 10.1109/ICCABS.2014.6863935
- Scopus: eid_2-s2.0-84908587423
- WOS: WOS:000361057400027
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Conference Paper: Reconstruction of influenza a virus variants from PacBio reads
| Title | Reconstruction of influenza a virus variants from PacBio reads |
|---|---|
| Authors | |
| Keywords | clustering PacBio viral quasispecies |
| Issue Date | 2014 |
| Citation | 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Miami, FL, 2-4 June 2014. In Conference Proceedings, 2014 How to Cite? |
| Abstract | © 2014 IEEE. Pacific Biosciences (PacBio) sequencing is providing thousands of reads with the length up to 10,000 bases. In most cases this length is enough to cover entire region of interest however this technology has high (≈ 15%) error rate. We propose a method for viral haplotype reconstruction generalizes k-means clustering with Hamming distance and capable of handling up to 25% random errors. When applied to PacBio reads from an Influenza A Virus (IAV) sample with ten variants, our method was able to reconstruct the four most frequent. |
| Persistent Identifier | http://hdl.handle.net/10722/285751 |
| ISBN | |
| ISI Accession Number ID |
| DC Field | Value | Language |
|---|---|---|
| dc.contributor.author | Artyomenko, Alexander | - |
| dc.contributor.author | Mangul, Serghei | - |
| dc.contributor.author | Wu, Nicholas C. | - |
| dc.contributor.author | Eskin, Eleazar | - |
| dc.contributor.author | Sun, Ren | - |
| dc.contributor.author | Zelikovsky, Alex | - |
| dc.date.accessioned | 2020-08-18T04:56:33Z | - |
| dc.date.available | 2020-08-18T04:56:33Z | - |
| dc.date.issued | 2014 | - |
| dc.identifier.citation | 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Miami, FL, 2-4 June 2014. In Conference Proceedings, 2014 | - |
| dc.identifier.isbn | 9781479957880 | - |
| dc.identifier.uri | http://hdl.handle.net/10722/285751 | - |
| dc.description.abstract | © 2014 IEEE. Pacific Biosciences (PacBio) sequencing is providing thousands of reads with the length up to 10,000 bases. In most cases this length is enough to cover entire region of interest however this technology has high (≈ 15%) error rate. We propose a method for viral haplotype reconstruction generalizes k-means clustering with Hamming distance and capable of handling up to 25% random errors. When applied to PacBio reads from an Influenza A Virus (IAV) sample with ten variants, our method was able to reconstruct the four most frequent. | - |
| dc.language | eng | - |
| dc.relation.ispartof | 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) | - |
| dc.subject | clustering | - |
| dc.subject | PacBio | - |
| dc.subject | viral quasispecies | - |
| dc.title | Reconstruction of influenza a virus variants from PacBio reads | - |
| dc.type | Conference_Paper | - |
| dc.description.nature | link_to_subscribed_fulltext | - |
| dc.identifier.doi | 10.1109/ICCABS.2014.6863935 | - |
| dc.identifier.scopus | eid_2-s2.0-84908587423 | - |
| dc.identifier.isi | WOS:000361057400027 | - |