VGA: A method for viral quasispecies assembly from ultra-deep sequencing data

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

*Corresponding author for this work

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

4 Scopus citations

Abstract

We present VGA, an accurate method for viral quasispecies assembly from ultra-deep sequencing data. The proposed method consists of a high-fidelity sequencing protocol and an accurate method for viral quasispecies assembly, referred to as Viral Genome Assembler (VGA). The proposed protocol is able to eliminate sequencing errors by using individual barcodes attached to the sequencing fragments. Results on both synthetic and real datasets show that our method able to accurately assemble HIV viral quasispecies and detect rare quasispecies previously undetectable due to sequencing errors. VGA outperforms state-of-the-art methods for the viral assembly. Furthermore, our method is the first viral assembly method which scales to millions of sequencing reads. Our tool VGA is freely available at http://genetics.cs.ucla.edu/vga/.

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

  • NGS
  • error-correction protocol
  • viral assembly
  • viral quasispecies

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Fingerprint Dive into the research topics of 'VGA: A method for viral quasispecies assembly from ultra-deep sequencing data'. Together they form a unique fingerprint.

Cite this