TTA Bioinformatics course Level 2


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

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