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- Publisher Website: 10.1109/ICCABS.2015.7344730
- Scopus: eid_2-s2.0-84960872775
- WOS: WOS:000377899500028
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Conference Paper: 2SNV: Quasispecies reconstruction from PacBio reads
| Title | 2SNV: Quasispecies reconstruction from PacBio reads |
|---|---|
| Authors | |
| Keywords | SNV PacBio viral quasispecies |
| Issue Date | 2015 |
| Citation | 2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Miami, FL, 15-17 October 2015. In Conference Proceedings, 2015 How to Cite? |
| Abstract | © 2015 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 using long SMRT reads. The proposed method based on correlation between SNVs and maximum likelihood for frequency estimation. When applied to PacBio reads from an Influenza A Virus (IAV) sample with ten variants, our method was able to reconstruct the nine most frequent. |
| Persistent Identifier | http://hdl.handle.net/10722/285765 |
| ISBN | |
| ISI Accession Number ID |
| DC Field | Value | Language |
|---|---|---|
| dc.contributor.author | Artyomenko, Alexander | - |
| dc.contributor.author | Wu, Nicholas C. | - |
| dc.contributor.author | Mangul, Serghei | - |
| dc.contributor.author | Eskin, Eleazar | - |
| dc.contributor.author | Sun, Ren | - |
| dc.contributor.author | Zelikovsky, Alex | - |
| dc.date.accessioned | 2020-08-18T04:56:35Z | - |
| dc.date.available | 2020-08-18T04:56:35Z | - |
| dc.date.issued | 2015 | - |
| dc.identifier.citation | 2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Miami, FL, 15-17 October 2015. In Conference Proceedings, 2015 | - |
| dc.identifier.isbn | 9781467396639 | - |
| dc.identifier.uri | http://hdl.handle.net/10722/285765 | - |
| dc.description.abstract | © 2015 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 using long SMRT reads. The proposed method based on correlation between SNVs and maximum likelihood for frequency estimation. When applied to PacBio reads from an Influenza A Virus (IAV) sample with ten variants, our method was able to reconstruct the nine most frequent. | - |
| dc.language | eng | - |
| dc.relation.ispartof | 2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) | - |
| dc.subject | SNV | - |
| dc.subject | PacBio | - |
| dc.subject | viral quasispecies | - |
| dc.title | 2SNV: Quasispecies reconstruction from PacBio reads | - |
| dc.type | Conference_Paper | - |
| dc.description.nature | link_to_subscribed_fulltext | - |
| dc.identifier.doi | 10.1109/ICCABS.2015.7344730 | - |
| dc.identifier.scopus | eid_2-s2.0-84960872775 | - |
| dc.identifier.isi | WOS:000377899500028 | - |