Long single-molecule reads can resolve the complexity of the Influenza virus composed of rare, closely related mutant variants

• DOI: 10.1101/036392
• Publication Date: 2016-01-14T00:31:21Z
• Authors: Alexander Artyomenko; Nicholas C Wu; Serghei Mangul; Eleazar Eskin; Ren Sun; Alex Zelikovsky
• Keywords: Benchmark (surveying)

Abstract As a result of high rate mutations and recombination events, an RNA-virus exists as heterogeneous “swarm” mutant variants. The long read length offered by single-molecule sequencing technologies allows each variant to be sequenced in single pass. However, error limits the ability reconstruct viral population composed rare, related In this paper, we present 2SNV, method able tolerate error-rate protocol 2SNV uses linkage between nucleotide variations efficiently distinguish them from errors. To benchmark sensitivity performed experiment on sample containing titrated level known Our is accurately clone with frequency 0.2% clones that differed only two nucleotides distantly located genome. outperforms existing methods for full-length reconstruction. open source implementation freely available download at http://alan.cs.gsu.edu/NGS/?q=content/2snv