Kenneth D Vernick | Search bioRxiv

bioRxiv2016

Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence data

We present user-friendly and adaptable software to provide biologists, clinical researchers and possibly diagnostic clinicians with the ability to robustly detect and reconstruct viral genomes from complex deep sequence datasets. A set of modular bioinformatic tools and workflows was implemented as the Metavisitor package 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 can be used on our Mississippi server, or can be installed on any Galaxy server instance and a pre-configured Metavisitor server image is provided. 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.

Bioinformatics↗

bioRxiv2016

Advancing insect vector biology research: a community survey for future directions, research applications and infrastructure requirements

BackgroundVector-borne pathogens impact public health and economies worldwide. It has long been recognized that research on arthropod vectors such as mosquitoes, ticks, sandflies and midges which transmit parasites and arboviruses to humans and economically important animals is crucial for development of new control measures that target transmission by the vector. While insecticides are an important part of this arsenal, appearance of resistance mechanisms is an increasing issue. Novel tools for genetic manipulation of vectors, use of Wolbachia endosymbiotic bacteria and other biological control mechanisms to prevent pathogen transmission have led to promising new intervention strategies. This has increased interest in vector biology and genetics as well as vector-pathogen interactions. Vector research is therefore at a crucial juncture, and strategic decisions on future research directions and research infrastructures will benefit from community input.\n\nMethodology/Principal FindingsA survey initiated by the European Horizon2020 INFRAVEC-2 consortium set out to canvass priorities in the vector biology research community and to determine key issues that should be addressed for researchers to efficiently study vectors, vector-pathogen interactions, as well as access the structures and services that allow such work to be carried out.\n\nConclusions/SignificanceWe summarize the key findings of the survey which in particular reflect priorities in European countries, and which will be of use to stakeholders that include researchers, government, and research organizations.\n\nAuthor SummaryResearch on arthropod vectors that transmit so-called arboviruses or parasites, such as mosquitoes, ticks, sandflies and midges is important for the development of control measures that target transmission of these pathogens. Important developments in this research area, for example vector genome sequencing, genome manipulation and use of transmission-blocking endosymbionts such as Wolbachia have increased interest in vector biology. As such, strategic decisions on research directions as well as research infrastructures will benefit from community input. A survey initiated by the European Horizon2020 INFRAVEC-2 consortium set out to investigate priorities in the vector biology research community as well as key issues that impact on research, and access to the structures and services that allow such studies to be carried out. Here we summarize the key findings of this survey, which in particular reflect priorities in European countries. The survey data will be of use to decision makers such as governments and research organizations, but also researchers and others in the field.

Scientific Communication and Education↗