title: QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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/.
  
  
  BACKGROUND
  ahnven@yahoo.it; ahnven@gmail.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610-3633, USA.
authors.forename: Mattia C F
authors.initials: MC
authors.lastname: Prosperi
authors.forename: Marco
authors.initials: M
authors.lastname: Salemi
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016415:Sequence Alignment; D012984:Software; D014780:Viruses / Q000145:classification / Q000235:genetics*
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