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

ABSTRACT:

Background

Next-generation sequencing (NGS) offers a unique opportunity for high-throughput genomics and has potential to replace Sanger sequencing in many fields, including de-novo sequencing, re-sequencing, meta-genomics, and characterisation of infectious pathogens, such as viral quasispecies. Although methodologies and software for whole genome assembly and genome variation analysis have been developed and refined for NGS data, reconstructing a viral quasispecies using NGS data remains a challenge. This application would be useful for analysing intra-host evolutionary pathways in relation to immune responses and antiretroviral therapy exposures. Here we introduce a set of formulae for the combinatorial analysis of a quasispecies, given a NGS re-sequencing experiment and an algo

SUBMITTER: Prosperi MC 

PROVIDER: S-EPMC3022557 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature