Venue: University of Oslo, Domus Medica, PC-stua (R211)
Application deadline: August 27th 2018
Please sign up for the course here.
This course is a continuation of TTA bioinformatics course level 1 and requires some basic knowledge of whole genome assembly, including quality assessment of raw data, trimming and contig assembly. Although not a strict requirement, we do recommend participants to attend in level 1 before signing up for this advanced course.
Participants of the hands-on session must bring their own laptops. A list of required preparations including instructions on how to install Geneious trial version will be provided end of August.
Part I: Seminars 11:00 – 12:30:
Theoretical introduction to the course and short repetition of required level 1 content.
11:00 – 11:30 Timo Lutter (TTA) – SNP calling, phylogenetic tree building and whole genome alignment
Nermin Zecic (TTA) – RNAseq and differential gene expression
11:30 – 12:00 Henrik Hasman – (Statens Serum Institut, DK) – Identification of acquired antibiotic resistance genes with ResFinder
12:00 – 12:30 Jon Bolin (FHI) – Mechanisms of foreign DNA acquisition and their detection in microbial genomes
12:30 – 13:00 Lunch
Part II: Hands-on exercises 13:00 – approx. 17:00:
Map to reference assembly and building SNP trees in Geneious with RAxML(using Ebola virus isolates as an example)
Basic alignments of bacterial genomes and draft genomes to detect large-scale evolutionary events (rearrangements/inversions) with Mauve
RNAseq and differential gene expression in Geneious
Introduction to Center for Genomic Epidemiology and ResFinder for identification of antimicrobial resistance genes