3rd Annual Training Course on Viral Bioinformatics and Genomics
Course dates: Monday 7th – Friday 11th of August 2017
Location: McCall Building, Garscube Campus, University of Glasgow, Glasgow, Scotland, UK
After the successful training courses in 2015 and 2016, the Viral Genomics & Bioinformatics team at the Centre for Virus Research (CVR) will be repeating the course this year. We will be giving a 5-day course, which will consist of a series of lectures and practical exercises that directly address bioinformatic challenges posed by the current surge of sequence data, with a focus on viral data sets and analyses. We will enable participants to understand and deal with high-throughput sequence datasets and encourage the exchange of ideas among diagnosticians, virologists, bioinformaticians and evolutionary biologists.
The 2017 course will introduce the participants to the power of the UNIX command-line and bash scripts, as well as a suite of bioinformatics tools covering the following topics with a focus on viral data sets:
- HTS sequencing technologies: overview of the different HTS platforms and sample preparations.
- The power of Unix: essential bash scripting.
- Reference assembly: aligning sequence reads to a known reference and visualizing the alignment (e.g. bowtie2, BWA, Tanoti, Tablet, UGENE).
- Variant calling: consensus sequence generation, low frequency variant calling and error correction (e.g. samtools, LoFreq, DiversiTools).
- De-novo assembly: overlap layout and de Bruijn graphs approaches for sequence assembly, quality assessment and merging contigs (e.g. ABySS, SPAdes, MIRA, IDBA-UD, QUAST, Mauve).
- Metagenomic analyses: sanitizing sequence datasets, assembling, annotating, visualizing (e.g. MetAMOS, Krona, DIAMOND, Kraken).
- Genomics: scaffolding, improving and finishing the assembly, gene annotation (e.g. ICORN, Artemis, RATT).
- Phylogenetic analysis: introduction to multiple sequence alignment and phylogenetic reconstruction (e.g. mafft, PhyML, FigTree).
Prerequisites
To maintain a good ratio of tutors to participants, the enrolment will be limited to 15 students. Preference will be given to applicants who: (1) have some familiarity with HTS technologies; (2) have already or are planning to generate viral HTS data in their work; and (3) have an interest in computers and programming (some basic experience in a command-line environment is necessary)
Registration Fee
£500 for the 5-day course including lunches and tea/coffee (participants are responsible for their own travel arrangements and accommodation). To apply, fill in the application form before the 30th of April 2017: http://goo.gl/TzSqxz. For more information and for those unable to access this Google application form, please see http://www.bioinformatics.cvr.ac.uk/.
MRC-University of Glasgow Centre for Virus Research
Sir Michael Stoker Building
Garscube Campus
Glasgow
G61 1QH
Scotland
UK
http://www.bioinformatics.cvr.ac.uk/
