2SNV: Quasispecies reconstruction from PacBio reads

Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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.

Original languageEnglish (US)
Title of host publication2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2015
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781467396639
DOIs
StatePublished - Dec 2 2015
Event5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2015 - Miami, United States
Duration: Oct 15 2015Oct 17 2015

Publication series

Name2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2015

Conference

Conference5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2015
CountryUnited States
CityMiami
Period10/15/1510/17/15

Keywords

  • PacBio
  • SNV
  • viral quasispecies

ASJC Scopus subject areas

  • Biotechnology
  • Computer Science Applications
  • Computational Mathematics
  • Medicine (miscellaneous)

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