Carissimo Guillaume, van den Beek Marius, Vernick Kenneth D, Antoniewski Christophe
Institut Pasteur, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, FRANCE.
CNRS, Unit of Hosts, Vectors and Pathogens (URA3012), Paris, FRANCE.
PLoS One. 2017 Jan 3;12(1):e0168397. doi: 10.1371/journal.pone.0168397. eCollection 2017.
Metavisitor is a software package that allows biologists and clinicians without specialized bioinformatics expertise to detect and assemble viral genomes from deep sequence datasets. The package is composed of a set of modular bioinformatic tools and workflows that are implemented in the Galaxy framework. Using the graphical Galaxy workflow editor, users with minimal computational skills can use existing Metavisitor workflows or adapt them to suit specific needs by adding or modifying analysis modules. Metavisitor works with DNA, RNA or small RNA sequencing data over a range of read lengths and can use a combination of de novo and guided approaches to assemble genomes from sequencing reads. We show that the software has the potential for quick diagnosis as well as discovery of viruses from a vast array of organisms. Importantly, we provide here executable Metavisitor use cases, which increase the accessibility and transparency of the software, ultimately enabling biologists or clinicians to focus on biological or medical questions.
Metavisitor是一个软件包，它使没有专业生物信息学专业知识的生物学家和临床医生能够从深度序列数据集中检测和组装病毒基因组。该软件包由一组模块化的生物信息学工具和工作流程组成，这些工具和流程在Galaxy框架中实现。使用图形化的Galaxy工作流程编辑器，计算技能有限的用户可以使用现有的Metavisitor工作流程，或者通过添加或修改分析模块来使其适应特定需求。Metavisitor可处理各种读长的DNA、RNA或小RNA测序数据，并可使用从头组装和引导组装方法相结合的方式从测序读数中组装基因组。我们表明，该软件具有快速诊断以及从大量生物体中发现病毒的潜力。重要的是，我们在此提供了可执行的Metavisitor用例，这提高了软件的可访问性和透明度，最终使生物学家或临床医生能够专注于生物学或医学问题。
