Application deadline 25th May
The need for effective and automated analyses of viral sequences has increased exponentially with the new high-¡©-throughput sequencing technologies. An understanding of the different bioinformatic approaches available for processing these data is an essential step in most virological studies. We will be giving a 5-¡©day course, which will consist of a series of lectures and practical exercises that directly address bioinformatic challenges posed by the current deluge of sequence data. We will enable participants to understand and deal with high-¡©- throughput sequence datasets and encourage the exchange of ideas among diagnosticians, virologists, bioinformaticians and evolutionary biologists.
The 2015 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.
- Unix primer: introduction to Bio-¡©-Linux 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., LoFreq, VPhaser).
- De-¡©-novo assembly: overlap layout and De Bruijn graphs approaches for sequence assembly; (e.g., Velvet, IDBA-¡©-UD).
- Metagenomic analyses: sanitizing sequence datasets, assembling, annotating, visualizing; (e.g., MetAMOS, Krona, MEGAN).
- Genomics: scaffolding, improving the assembly, finishing the assembly, gene annotation; (e.g., ICORN, Artemis).
- Phylogenetic analysis: introduction to multiple sequence alignment and phylogenetic reconstruction; (e.g., clustal, PhyML).
The course will be held at the CVR, Garscube Campus, University of Glasgow, Glasgow, UK. The CVR has been designated an World Organisation for Animal Health (OIE) Collaborating Centre for Viral Genomics and
Bioinformatics at the 82nd OIE General Session
Click to download for more information http://bioinformatics.cvr.ac.uk/Downloads/OIE_announcements.pdf
Charles Masembe (BVM, MSc., PhD),
Associate Professor (Molecular Genetics & Evolution),
Wellcome Trust Fellow,