Diana Karina Diaz Canova, PhD student at the University of Tromsø, recently received funding from IBA to attend a course on Viral Bioinformatics and Genomics in Scottland.
She just came back, and you can read under what she says about her research and the bioinformatic training course!
My PhD research project is focused on improving MVA-vectored vaccine safety by determining potential recombination between MVA-vectored vaccine and naturally occurring Fennoscandian cowpox viruses (CPXVs) during coinfection/superinfection of mammalian cells. The risk of recombination is considered low because MVA multiplies poorly in most mammalian cells. However, we have demonstrated recombination occurred between MVA vaccine vector and CPXV. As part of my PhD project, I will analyse the genomes of hybrid progeny viruses from recombination between MVA – vectored vaccine and Cowpox virus. These genomes were sequenced by Next Generation Sequencing technology. However, successful analysis of these genomes sequences requires a good knowledge of bioinformatics analyses.
Therefore, I was motivated to attend the 5th Annual Training Course on Viral Bioinformatics and Genomics (19-23rd Aug 2019) organised by the Medical Research Council (MRC) – University of Glasgow Centre for Virus Research (CVR). I believed that attending the course will equip me with the right bioinformatic tools and also the impetus to analyse my sequence data.
The course was focused in analysing high-throughput sequence (HTS) datasets using bioinformatics tools, UNIX command-line and bash scripts. During the five-day course, different topics such as HTS sequencing technologies, reference assembly, variant calling, de novo assembly, metagenomics analyses, phylogenetic analysis etc. were covered through lectures and practical sessions.
The course was well structured and organized in such a way making it easy to comprehend for participants, like me with basic experience of UNIX command lines. The course coordinators dedicated the first day to introduce the UNIX command lines. In addition, after every lecture we had a practical session where we could put what we have learnt into practice. During the practical sessions, we analysed viral genome sequences using different bioinformatics tools.
The instructors used fun and creative ways such as Lego building for teaching reference assembly. The courses instructors were not only bioinformaticians but have extensive knowledge and real hands on experience in viral genome sequence analysis. This was quite helpful because we could discuss the current challenges we are facing in our individual project with them. I have got some feedback which I intend incorporating into my subsequent analysis.
Attending the course was a good and rewarding experience. Although the five days course was intensive, it was at the same time very productive because I could learn the main bioinformatics tools that are relevant to achieve the goals of my PhD research project.
I would like to thank to the National Graduate School in Infection Biology and Antimicrobials (IBA) for grating me the travel grant assistance to attend this course.