3rd Viral Bioinformatics and Genomics Training Course (7th – 11th August 2017)

For the 3rd year running, we have held our Viral Bioinformatics and Genomics training course at the Garscube campus of the University of Glasgow. The course took place from Monday 7th August – Friday 11th August 2017, with 16 participants attending from academic and health institutions from across the UK, Europe, USA, Uganda, and Saudi Arabia.

The course timetable was tweaked a little from the 1st and 2nd courses in previous years to include an introductory transcriptomics session, as well as poster and wine reception at the Centre for Virus Research (CVR). 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, 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. The course was organized this year by Richard Orton ably assited by Quan Gu, with help from Andrew Davison, Ana Filipe, Joseph Hughes, Maha Maabar, Sejal Modha, David Robertson, and Sreenu Vattipally. Quan Gu will be organizing the 4th instalment of the course in August 2018.

Day 1 – Introductions, Quality Control, and Reference Assembly

The course started off with an introduction to Viral Bioinformatics from our new 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.

Day 2 – Consensus/Variant Calling, and 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 & Phylogenetic Analysis

On the 3rd day, participants learnt 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, Genome Annotation, and Metagenomics

On the 4th day, the course moved on to metagenomics analyses, with sessions on de novo assembly and the different assemblers available, assessing the quality of contigs, merging and gap filling. After sessions on annotation transfer and the MetAMOS metagenomics pipeline, all course participants and instructors moved on to Brel restaurant for our annual course dinner and drinks in the evening with our very own CEO.

Day 5 – Pipelines

The final day involved a build your own pipeline session in the morning, followed by optional sessions in the afternoon including transcriptomics, haplotype reconstruction, taxonomy, and kmer based metagenomics, 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, and thanks for making it such an enjoyable course.

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