Course: Introduction to Viral Bioinformatics

Where: Glasgow, UK

When: Monday 15th June - Friday 19th June 2026

Webpage:
https://bioinformatics.cvr.ac.uk/training/introduction-to-viral-bioinformatics-training-course-2026/

Applications are now open for our annual training course in Viral
Bioinformatics. 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. Topics
covered in the course 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, viral
      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) high-throughput sequencing on
      different platforms
  *   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 analyses
  *   Bash scripting: writing simple bash scripts to automate common
      bioinformatic procedures

For more details including information on how to apply see the webpage:
https://bioinformatics.cvr.ac.uk/training/introduction-to-viral-bioinformatics-training-course-2026/

Richard Orton <Richard.Orton@glasgow.ac.uk>

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