期刊
BRIEFINGS IN BIOINFORMATICS
卷 21, 期 5, 页码 1766-1775出版社
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbz086
关键词
viral quasispecies; Illumina sequencing platform; analysis workf low; open-source software; sub-consensus SNV; haplotype reconstruction
资金
- Agencia Nacional de Promocion Cientifica y Tecnologica [PICT 2014982, PICT 2017-2581]
- Instituto Nacional de Tecnologia Agropecuaria [PNSA 1115052]
Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workf low proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach.
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