Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing.

摘要: Background Next-generation sequencing (NGS) offers a unique opportunity for high-throughput genomics and has potential to replace Sanger in many fields, including de-novo sequencing, re-sequencing, meta-genomics, characterisation of infectious pathogens, such as viral quasispecies. Although methodologies software whole genome assembly variation analysis have been developed refined NGS data, reconstructing quasispecies using data remains challenge. This application would be useful analysing intra-host evolutionary pathways relation immune responses antiretroviral therapy exposures. Here we introduce set formulae the combinatorial quasispecies, given re-sequencing experiment an algorithm reconstruction. We require that sequenced fragments are aligned against reference genome, is partitioned into sliding windows (amplicons). The reconstruction based on combinations multinomial distributions designed minimise false variants, called in-silico recombinants.