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Bioinformatics. 2012 Jan 1;28(1):132-3. doi: 10.1093/bioinformatics/btr627. Epub 2011 Nov 15.

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.

Author information

1
Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610-3633, USA.

Abstract

SUMMARY:

Next-generation sequencing (NGS) is an ideal framework for the characterization of highly variable pathogens, with a deep resolution able to capture minority variants. However, the reconstruction of all variants of a viral population infecting a host is a challenging task for genome regions larger than the average NGS read length. QuRe is a program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) NGS data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral variants overlapping across the genome division. QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions.

AVAILABILITY:

QuRe is platform-independent, multi-threaded software implemented in Java. It is distributed under the GNU General Public License, available at https://sourceforge.net/projects/qure/.

CONTACT:

ahnven@yahoo.it; ahnven@gmail.com

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
22088846
PMCID:
PMC3244773
DOI:
10.1093/bioinformatics/btr627
[Indexed for MEDLINE]
Free PMC Article

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