4th Annual Training Course on
Viral Bioinformatics and Genomics
(20-24th Aug, 2018)
The MRC-University of Glasgow Centre for Virus Research (CVR) has been running a successful training course on Viral Bioinformatics and Genomics annually since 2015 and applications are now open for the 2018 course. 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. Students will work on our high performance computing facilities at the CVR. The CVR has been designated an OIE Collaborating Centre for Viral Genomics and Bioinformatics at the 82nd OIE General Session.
The 2018 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:
- 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. Muscle, PhyML, FigTree).
Students will work on our high performance computing facilities at the CVR and be given the time to analyse their own datasets under the guidance of the instructors.
To maintain a good ratio of tutors to participants, the enrolment will be limited to 16 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)
Quan Gu (Course Organiser), Sreenu Vattipally (Course Organiser), Andrew Davison, Ana Da Silva Filipe, Joseph Hughes, Richard Orton, David Robertson
£500 for the 5-day course including lunches and tea/coffee breaks (NB: participants are responsible for their own travel arrangements and accommodation).
To apply, please fill in the online application form
before 20th April 2018
For more information and for those unable to access this Google application form, please contact Dr. Quan Gu(firstname.lastname@example.org). You will be contacted within two weeks of the deadline if you have been shortlisted for the course this year.
Course dates: Monday 20th – Friday 24th of August 2018
Location: McCall Building, Garscube Campus, University of Glasgow, Glasgow, Scotland, UK