Introduction to Viral Bioinformatics Training Course 2026

• PLEASE NOTE – COURSE APPLICATIONS ARE NOT CURRENTLY LIVE- THEY WILL BE SOON – LATE JANUARY 2026

The Medical Research Council-University of Glasgow Centre for Virus Research (CVR) has been organising an annual training course on Viral Bioinformatics since 2015 and applications are currently open for the 2026 course which will run from Monday 15th June (9am start) to Friday 19th June (12.30 finish).

The course offers a comprehensive introduction to Viral Bioinformatics and comprises a 4.5 day program including lectures and practical exercises tailored towards viral high throughput sequencing data sets. The course is taught by members of the CVR bioinformatics team who have a wealth of experience on a broad range of virological research questions. As this is an introductory course, it is primarily aimed at people who have little command line bioinformatics experience – topics covered include:

• Linux command line: introduction to working with the command line, navigating the file system and manipulating files
• NGS reads and QC: introduction to next generation sequencing, FASTQ reads, read trimming and quality control (trim_galore, FASTQC)
• Reference assembly: aligning reads to a known reference, SAM/BAM file manipulation and visualisation (bwa, samtools, tablet)
• Consensus calling: consensus sequence generation and variant calling (samtools, ivar, lofreq)
• Phylogenetic analysis: introduction to multiple sequence alignment, phylogenetic reconstruction and visualisation (mafft, clustal, raxml, figtree)
• Metagenomics: de-novo assembly and quality assessment, contig taxonomic classification and visualisation, and rapid k-mer based metagenomics (spades, idba, quast, diamond, krona, kraken)
• Genomics: a dedicated session with the CVR genomics team who do a huge range of viral (and host) bioinformatics sequencing
• Nanopore: introduction to reference alignment and consensus calling for Oxford Nanopore (MinION) data (minimap, samtools, medaka)
• nf-core/viralrecon: introduction to using the nextflow nf-core viral bioinformatics pipeline to run common viral bioinformatics pipelines 
• Bash scripting: writing simple bash scripts to automate common bioinformatic procedures
  

The main prerequisite is that you are either currently (or soon to be) working on viruses and viral data sets – if you are working only on bacteria or only host data then this is probably not the course for you.

This is an introductory course, covering many basic concepts such as command line navigation, FASTQ format, SAM/BAM file creation, de novo assembly etc – therefore if you are already a fully fledged bioinformatician with extensive command line experience this may not be the course for you, but you are more than welcome to get in touch if you are still interested in attending after reading the topics covered above.

Cost

The cost of the course is £600 for the 4.5-day course including lunches and tea/coffee at breaks – please note participants are responsible for their own travel arrangements and accommodation.  During the course we also include a couple of social events in the evening (typically the Tuesday and Thursday night) which include a free food.

Application

To apply, please fill in the online application form which will stay open until the 30th of April: WILL BE LIVE IN LATE JANUARY 2026

Candidates will be selected/reviewed on a **rolling basis** within a few weeks of applying to enable ample time for you to arrange travel and accommodation. If you are successful, you will have one month to pay the registration fee to guarantee a place on the course. We typically select 18 people to attend the course.