Advanced Whole Genome Sequence Analysis for Microbial Diagnostics
Do you already have a good understanding of WGS and how to analyse the data using online web-services or software with a graphical user interface? Do you want to take your analyses to the next level for optimal flexibility, control, speed, and autonomy? During this workshop we will mainly be working commandline in a Linux environment. No prior experience working commandline is necessary. The workshop spans 2 full days (9:00-17:00) and includes the following:
- Initialising and accessing a personal Linux environment via Amazon Cloud
- Installing/running software in a Linux environment (including repositories and Docker)
- Generating small bash-scripts to run multiple methods in a pipeline or analyse batches of files
- Checking the quality of raw reads with FastQC
- Trimming of raw reads with Cutadapt
- Performing assembly of draft genomes using Shovill and SPAdes and evaluate the quality of the draft genomes
- Mapping of reads to draft or reference genomes using BWA to calculate depth of coverage, identify snps and contaminating reads
- Running the methods from Center for Genomic Epidemiology commandline with updated or customised databases
- Generating phylogenetic trees commandline and visualising the results
Organiser and main teacher: Mette Voldby Larsen
Price: Fee for participating in the workshop is 775 EUR + VAT. Early birds get a 100 EUR discount. The fee covers the workshop, breakfast, lunch, coffee, and afternoon snacks all workshop days. It does not include dinner, travel or accommodation.
Location: Conference Center and Hotel Rungstedgaard, Rungsted Kyst, Denmark. Hotel rooms are available for 135 EUR + VAT per night.
Audience: Microbiologists, molecular biologists, PhD students etc. with prior knowledge of WGS, but no or limited experience working in a commandline Linux environment. For full learning outcome participants are required to bring their own laptop.
Number of participants: Max 10 participants.
Next workshop: 5th-6th of Nov. 2018. Early bird deadline is 3rd Aug. 2018. Final deadline is 5th Oct. 2018.
Download preliminary workshop schedule Nov. 2018: TBA
Note: Please contact us if you are 10 or more colleagues interested in participating. We might be able to arrange the workshop coming to you instead of the other way around.