Periodic Reporting for period 2 - VIROGENESIS (Virus discovery and epidemic tracing from high throughput metagenomic sequencing)
Reporting period: 2016-12-01 to 2018-05-31
As a final result, the VIROGENESIS project has delivered novel methodology and software solutions for NGS virome analysis, ranging from fast and accurate assembly and identification of known and unknown viral pathogens to modelling and inferring their spread in time and space. These developments have been accompanied by interactive and informative visualisations and dynamic graphical user interfaces. VIROGENESIS tools have been designed to be versatile and user-friendly, and proven to outperform other existing and well-known methods in terms of sensitivity and accuracy, based on a range of simulated and real genomic data. The software developed offers scalability to work with large datasets and allows user exploitation on a routine basis. The VIROGENESIS project aimed at maximizing the concept of open source software, which is also easy to install and adapt, accompanied with detailed documentation and which can run on the most popular operating systems by their platform-independence. Therefore, these characteristics of VIROGENESIS tools support the objective of becoming standard tools for virome analysis in this rapidly evolving research field. In addition, novel opportunities for innovation and commercialization of bioinformatics products have been established.
Second, the organisation of international workshops in Europe where a wide range of VIROGENESIS software will be used in theoretical and practical sessions strengthen the role of Europe in developing novel and innovative solutions addressing persistent challenges of NGS virome analyses. This is not only demonstrated by the impact of VIROGENESIS publications, but also by the interactions established with external partners, and with other research initiatives. Novel interactions were established to transfer knowledge and technologies from other research fields, e.g. geospatial situational awareness, into the field of epidemic tracking in order to create new opportunities.
Third, VIROGENESIS has facilitated research and innovation opportunities for SMEs as well as the commercialization of bioinformatics products. In addition to the impact initially foreseen, recent advances in VIROGENESIS technology and recent discoveries within the project have given rise to new applications, with new innovations filed in a European and US patent applications. Next, novel business opportunities for SMEs have been identified by transferring and adapting VIROGENESIS software for analyses of bacteria. By partnering with existing analysis platforms with a wide user base, VIROGENESIS will not have only guaranteed long life of the VIROGENESIS tools, but also help the open source bioinformatics suite to grow and be one of the top players as a commercial product.
Fourth, by teaching students from all over the world attending the training sessions of the highly regarded VEME workshops, these students can bring back knowledge of these tools to their own institutions, thus promoting global use. Furthermore, new methods and tools have been disseminated via a large collection of scientific publications. A VIROGENESIS pipeline tool has been implemented in the UGENE platform which will allow wide dissemination of our tool, including to researchers who computational resources and/or programming skills are modest.