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BMCBI
2011

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

8 years 10 months ago
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing
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, metagenomics, 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 algorithm for quasispecies reconstruction. We require that sequenced fragments are aligned against a reference genome, and that the reference genome is partitioned into a set of sliding windows (amplicons). The ...
Mattia C. F. Prosperi, Luciano Prosperi, Alessandr
Added 24 Aug 2011
Updated 24 Aug 2011
Type Journal
Year 2011
Where BMCBI
Authors Mattia C. F. Prosperi, Luciano Prosperi, Alessandro Bruselles, Isabella Abbate, Gabriella Rozera, Donatella Vincenti, Maria Carmela Solmone, Maria Rosaria Capobianchi, Giovanni Ulivi
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