Drs. James Wasmuth (VetMed) & Tarah Lynch (Medicine) are putting on a Genome Informatics course for the Fall 2018 semester.

We are soliciting applications from students interested in taking the course. Numbers are limited. Interested postdocs and staff are also welcome to apply. Priority will be given to students taking the course for credit.

Please tell me the graduate program in which you are enrolled and whether you’ll be taking the course for credit or auditing. If you haven’t received a confirmation of your email within two working days, please send me another email, in case it ends up in my email’s clutter folder. We will pick the students in the first week of August.

Course Motivation
Large-scale genomics has traditionally been the preserve of researchers at large genome-centres. The cost of sequencing DNA has decreased to a point at which modest-sized labs are sequencing the genomes of their favourite organisms. The bottleneck is in the processing and analysis of these data. One reason is a shortage in expertise in working with genome-scale data. Many researchers rely on expensive software solutions and consider the analysis methods as a black box. It is important that our students receive the necessary training to use the latest software, understanding the methods/algorithms and interpreting the results appropriately.

Not human-centric
The focus on the course will be on the genomes of pathogenic bacteria and eukaryotes. There are many external courses available on working with the human genome. Working with non-human data comes with its own nuances and problems. Sadly, there is not enough time for everything. 

Topics include:
Genome sequence technologies
Assembling genomes
Annotating assemblies
Differential expression of genes
Transcript-based assemblies and annotations
Variant (SNP/SV) calling
Command line tools for data processing
subject to change

We ask that attendees have a working knowledge of the linux command line. There are several online tutorials, including: codecademy.