3rd Annual Training Course on
Viral Bioinformatics and Genomics

The application deadline (30th April 2017) for this year's course has now passed, so we are unable to accept more applications; applicants will be contacted within 2 weeks of the deadline about places on this year's course, if you have any queries please contact Richard.Orton@glasgow.ac.uk. To be kept informed of future courses, please click here.

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. 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 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:

  • 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)

Instructors

Richard Orton (Course Organiser), Quan Gu (Course Organiser), Andrew Davison, Ana Da Silva Filipe, Joseph Hughes, Maha Maabar, Sejal Modha, Sreenu Vattipally.

Application

The application deadline (30th April 2017) for this year's course has now passed so we are unable to accept more applications, if you have any queries please contact Richard.Orton@glasgow.ac.uk. To be kept informed of future courses, please click here.

Cost

The 5 day course costs £500 including lunches and refreshments. Please note, participants are responsible for their own travel arrangements and accommodation.

Previous Courses

More details on our previous courses, including timetables, are available on our blog: 2015 course and 2016 course.

Course Poster

Course posters for displaying on notice boards are available here and here.

CVR

The CVR has been designated an OIE Collaborating Centre for Viral Genomics and Bioinformatics at the 82nd OIE General Session.


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





















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