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Discovering and sequencing new plant viral genomes by next‐generation sequencing: description of a practical pipeline
Author(s) -
Blawid R.,
Silva J.M.F.,
Nagata T.
Publication year - 2017
Publication title -
annals of applied biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.677
H-Index - 80
eISSN - 1744-7348
pISSN - 0003-4746
DOI - 10.1111/aab.12345
Subject(s) - biology , dna sequencing , genome , computational biology , pipeline (software) , sequence assembly , genetics , computer science , dna , gene , gene expression , transcriptome , programming language
Small‐scale sequencing has improved substantially in recent decades, culminating in the development of next‐generation sequencing (NGS) technologies. Modern NGS methods have helped the discovery of many new plant viruses. Nevertheless, there is still a need to establish solid assembly pipelines targeting small genomes characterised by low identities to known viral sequences. Here, we describe and discuss the fundamental steps required for discovering and sequencing new plant viral genomes by NGS. A practical pipeline and standard alternative tools used in NGS analysis are presented.