4th Annual Training Course on Viral Bioinformatics and Genomics (20-24th Aug, 2018)

From 20-24th Aug, we have held our 4th Viral Bioinformatics and Genomics training course at the Garscube campus of the University of Glasgow. In this year, our course had 16 participants attending from academic and health institutions from across the UK, Europe, Canada, Australia, Qatar, and South Africa. The MRC-University of Glasgow Centre for Virus Research (CVR) has been designated a World Organisation for Animal Health (OIE) Collaborating Centre for Viral Genomics and Bioinformatics at the 82nd OIE General Session.

Instructors:

Andrew Davison, Ana Filipe, Quan Gu (Course Organiser), Joseph Hughes, Richard Orton, David Robertson, Sreenu Vattipally (Co-organiser)

The course involved the usual suspects of instructors, and included sessions on Linux, reference assembly and consensus/variant calling, advanced bash scripting, de novo assembly, metagenomics, transcriptomics, genome annotation, and phylogenetics, all with a focus on viral data sets. The course itself was held in the IAMS computer room of the McCall building, with lunch and refreshments in the Mary Stewart building, poster session in the Sir Michael Stoker building, and the course dinner at Brel restaurant.

Day 1: Introductions, NGS Reads, and Mapping

The course started off with an introduction to Viral Bioinformatics from our head of bioinformatics Prof. David Robertson followed by an introduction to High Throughput Sequencing (HTS) by the head of the CVR’s sequencing facility Ana Filipe. This was followed by a 1 minute – 1 slide introduction session involving all course participants and instructors.In the afternoon, there were sessions on Basic Linux Commands, NGS Reads & Cleaning, and Mapping Reads to a Reference, followed by a wine and poster reception held at the CVR where participants got a chance to get know each other and the instructors better, and discuss the latest viral research with members of the CVR. The Director of CVR Prof. Massimo Palmarini came to the wine reception to give us a speech.

Day 2: Variant Calling & Advanced Linux

The course picked up from the previous day with sessions on Post Assembly & Consensus Calling followed by Low-Frequency Variant Calling. In the afternoon, the course moved on to advanced Linux topics with sessions covering the basics of text processing, scripts, and Linux conditions.

Day 3 – Bash Scripting and Phylogenetic Analysis

On the 3rd day, participants learned how to build their own bash scripts involving loops and arrays to automate sample analysis, whilst in the afternoon there were sessions on automatically downloading sequence data from Genbank followed by sequence alignment and phylogenetic analysis.

Day 4 – De Novo Assembly and Genome Annotation

On the 4th day, the course moved on to de novo assembly analyses, and the different assemblers available, assessing the quality of contigs, merging and gap filling. In the coffee break, we are playing the lego of alignment. In the evening, all course participants and instructors moved on to Brel restaurant for our annual course dinner and drinks. Quan Gu showed his singing skill during the dinner.

Day 5 – Metagenomics, Transcriptomics, and Pipelines

The final day involved metagenomics, transcriptomics and a build your own pipeline session in the morning, as well as a chance to discuss participants own data. After our annual cutting of the OIE cake, we said our goodbyes to this year’s participants. We wish all the participants lots of fun with their new bioinformatic skills.

If you are interested in finding out about future course that we will be running, please fill in the form with your details.