5th Annual Training Course on Viral Bioinformatics and Genomics (19-23rd Aug, 2019)

5th Annual Training Course on Viral Bioinformatics and Genomics (19-23rd Aug, 2019)

McCall Building, Garscube Campus, University of Glasgow, Glasgow, Scotland, UK
19 Aug 2019

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. Applications are now open for the 2019 course. This 5-day course consists of a series of lectures and practical exercises that directly address viral bioinformatic challenges posed by the current surge of sequence data. Participants will understand and deal with high-throughput sequence datasets. This course also encourages the exchange of ideas among diagnosticians, virologists, bioinformaticians and evolutionary biologists. 

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

The 2019 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.
  • Introduction to Unix and 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).
  • Transcriptomics: Overview of viral transcriptomics and current analysis methods.


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) 


Sreenu Vattipally (Course Organiser), Srikeerthana Kuchi (Course Organiser), Salvatore Camiolo, Ana Da Silva Filipe, Quan Gu, Joseph Hughes, Richard Orton, David Robertson, Josh Singer and Derek Wright


£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 30th April 2019. You will be contacted within two weeks after the deadline if you have been shortlisted for the course.

For more information and for those unable to access this Google application form, please contact Dr. Sreenu Vattipally (sreenu.vattipally@glasgow.ac.uk).

Application deadline: 30th April 2019 
Course dates: Monday 19th – Friday 23rd of August 2019 
Location: McCall Building, Garscube Campus, University of Glasgow, Glasgow, Scotland, UK