6th Annual training course on Viral Bioinformatics and Genomics (21 – 25 August 2023)
- Post by: Sreenu Vattipally
- April 13, 2023
- No Comment
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 and applications are now open for the 2023 course. This will be 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 datasets and analyses. We will enable participants to understand and deal with high-throughput sequence (HTS) datasets and encourage the exchange of ideas and collaborations among diagnosticians, virologists, bioinformaticians and evolutionary biologists. Trainees will work on our high-performance computing facilities at the CVR and will be given the time to analyze their own datasets under the guidance of the instructors.
The 2023 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, 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).
- Metagenomic analyses: sanitizing sequence datasets, assembling, annotating, visualization (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).
Prerequisites
To maintain a good ratio of tutors to participants, the enrollment 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 a prerequisite)
Instructors
Ana Da Silva Filipe, David Robertson, Derek Wright, Joseph Hughes (Course Organizer), Quan Gu, Richard Orton, Sreenu Vattipally, Srikeerthana Kuchi (Course Organizer)
Registration
£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 2023
For more information and for those unable to access this Google application form, please see CVR Bioinformatics. You will be contacted within two weeks of the deadline if you have been shortlisted for the course this year.
Location: Boyd Orr building, University of Glasgow, United Kingdom