Viral bioinformatics training course 2024

7th Annual training course on Viral Bioinformatics and Genomics (24 – 28 June 2024) 

‌Location: Garscube campus, University of Glasgow, United Kingdom 

The MRC-University of Glasgow Centre for Virus Research (CVR) has been organizing an annual training course on Viral Bioinformatics and Genomics since 2015. Applications are currently open for the 2024 course, offering a comprehensive 5-day program comprising lectures and practical exercises tailored to confront bioinformatic challenges associated with high throughput sequencing. With a specialized emphasis on viral datasets and their analyses, this course is taught by bioinformaticians who have ample experience on addressing a broad range of virological problems. Past courses have fostered collaboration among participants who often come from varied backgrounds, e.g., diagnosticians, virologists, bioinformaticians, and evolutionary biologists. 

The 2024 course will introduce the participants to the UNIX OS and Bash scripting along with a suite of bioinformatics tools covering the following topics:

  • HTS sequencing technologies: overview of the different HTS platforms and sample preparations. 
  • Unix OS: introduction to Unix OS and essential Bash scripting.
  • Reference assembly: aligning sequence reads to a known reference and visualization (e.g., bowtie2, BWA, Tablet, UGENE).
  • Variant calling: consensus sequence generation, low frequency variant calling and error correction (e.g., samtools, LoFreq, DiversiTools).
  • Phylogenetic analysis: introduction to multiple sequence alignment and phylogenetic reconstruction (e.g., MAFFT, PhyML, FigTree).
  • Visualization in R (e.g., ggplot) 
  • Choice between the following omics modules:
    • Transcriptomics analyses: read alignment (e.g., Hisat2), differential gene expression analysis (e.g., edgeR, DESeq2), downstream functional analysis (e.g., Reactome, DAVID). 
    • Metagenomic analyses: sanitizing sequence datasets, de-novo assembly and quality assessment (e.g., ABySS, SPAdes, MIRA, IDBA-UD, QUAST), annotating, classification and visualization (e.g., MetAMOS, Krona, DIAMOND, Kraken). 
 
Prerequisites 

To maintain a good ratio of tutors to participants, the enrollment will be limited to 20 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 a prerequisite)  

Instructors 

Ana Da Silva Filipe, David Robertson, Derek Wright (Course co-organizer), Joseph Hughes (Course Organizer), Quan Gu, Richard Orton, Sreenu Vattipally, Srikeerthana Kuchi. 

Registration 

£600 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 which will stay open until the 30th of April: https://bit.ly/vgb2024 

Candidates will be selected on a rolling basis within a month of submitting their application. If you have been accepted on the course, you will have one month to pay the registration fee to guarantee your place on the course.