Targeted virus detection in next-generation sequencing data using an automated e-probe based approach

被引：18
作者：
Visser, Marike [1 ,2 ]
Burger, Johan T. [2 ]
Maree, Hans J. [1 ,2 ]
机构：
[1] Agr Res Council, Infruitec Nietvoorbij Inst Deciduous Fruit Vines, Stellenbosch, South Africa
[2] Univ Stellenbosch, Dept Genet, ZA-7600 Stellenbosch, South Africa
来源：
VIROLOGY | 2016年 / 495卷
基金：
新加坡国家研究基金会;
关键词：
Bioinformatics; Grapevine; Grapevine leafroll disease; High-throughput sequencing; Virus diagnostics; ALIGNMENT; PIPELINE; VIROME;
D O I：
10.1016/j.virol.2016.05.008
中图分类号：
Q93 [微生物学];
学科分类号：
071005 ; 100705 ;
摘要：
The use of next-generation sequencing for plant virus detection is rapidly expanding, necessitating the development of bioinformatic pipelines to support analysis of these large datasets. Pipelines need to be easy implementable to mitigate potential insufficient computational infrastructure and/or skills. In this study user-friendly software was developed for the targeted detection of plant viruses based on e-probes. It can be used for both custom e-probe design, as well as screening preloaded probes against raw NGS data for virus detection. The pipeline was compared to de novo assembly-based virus detection in grapevine and produced comparable results, requiring less time and computational resources. The software, named Truffle, is available for the design and screening of e-probes tailored for user-specific virus species and data, along with preloaded probe-sets for grapevine virus detection. (C) 2016 Elsevier Inc. All rights reserved.
引用
收藏
页码：122 / 128
页数：7
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