Reconstruction of influenza a virus variants from PacBio reads

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

*Corresponding author for this work

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

1 Scopus citations

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 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.

Original languageEnglish (US)
Title of host publication2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781479957866
DOIs
StatePublished - Jul 24 2014
Event2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014 - Miami, United States
Duration: Jun 2 2014Jun 4 2014

Publication series

Name2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014

Other

Other2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014
CountryUnited States
CityMiami
Period6/2/146/4/14

Keywords

  • PacBio
  • clustering
  • viral quasispecies

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

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