2nd Annual Training Course on Viral Bioinformatics and Genomics
Course dates: 1st-5th of August 2016
Location: Garscube Campus, University of Glasgow, Glasgow, UK
After the successful training course in 2015, the Viral Genomics & Bioinformatics team at the Centre for Virus Research 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 deluge of sequence data. 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 2016 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., LoFreq, VPhaser).
- De-novo assembly: overlap layout and De Bruijn graphs approaches for sequence assembly; (e.g., Velvet, IDBA-UD).
- Metagenomic analyses: sanitizing sequence datasets, assembling, annotating, visualizing; (e.g., MetAMOS, Krona, MEGAN).
- Genomics: scaffolding, improving the assembly, finishing the assembly, gene annotation; (e.g., ICORN, Artemis).
- Phylogenetic analysis: introduction to multiple sequence alignment and phylogenetic reconstruction; (e.g., clustal, PhyML).
Students will work on our high performance computing facilities at the Centre for Virus Research (CVR) and be given the time to analyse their own datasets under the guidance of the instructors. For details of the 2015 course: http://goo.gl/O4zAVs.
Instructors:
Andrew Davison
Joseph Hughes (Course Organiser)
Sejal Modha
Richard Orton (Course Organiser)
Sreenu Vattipally
Gavin Wilkie
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:
- have some familiarity with HTS technologies
- have already or are planning to generate HTS in their work
- have an interest in computers and programming (some basic experience in a command-line environment is necessary)
Registration fee:
£450 for the 5-day course including lunches. To apply fill in the questionnaire before the 18th of March [ http://goo.gl/forms/TKq5YlFZGJ ]. You will be contacted within a week of the deadline if you have been shortlisted for the course this year.
NB: Participants are responsible for their own travel arrangements and accommodation
Our Address
MRC-University of Glasgow Centre for Virus Research
Garscube Campus, Stoker Building, G61 1QH
Scotland
http://www.bioinformatics.cvr.ac.uk/
