For ACENET training workshops, please see Workshops & Seminars.
The new Compute Canada national general purpose systems, Graham and Cedar, have massive compute resources that are available to all Canadian research teams. Focusing on Graham, located at the University of Waterloo, this online seminar provides an overview of available systems, and basic usage information including job submissions/management, queueing policies and available software and support. No registration is required. Join the seminar at SN-Seminars Vidyo room
Note: In order to receive audio/video you will need to install the Vidyo plugin (Windows, Mac, Linux, iPhone, Android), which should download automatically when you follow the above link. If you run into problems, please email email@example.com. It is highly recommended that you join the seminar a few minutes early to ensure Vidyo is working before the meeting starts.
This session will provide a basic introduction to using Linux and the command-line interface in order to access Compute Canada high performance computing (HPC) resources. Topics covered include the basics of computing with high performance computers, filesystem hierarchy, basic linux commands for navigating filesystem, basic linux commands for file handling, using the manual command to get more details on linux command line options, and downloading and decompressing files from the internet.
This session is for anyone interested in learning Linux or using Compute Canada / WestGrid resources. If you do not have a Compute Canada account, a guest account can be created for you for use during this session.
This is an introductory-level session. No prior knowledge or experience is required.
Next generation sequencing (NGS) has allowed for the quick turn around time of whole genome and transcriptome sequencing of cancer patients, which enables a detailed look at somatic changes in tumours. However, there are many confounding factors in the identification in mutations, structural changes and gene expression changes, such as systematic bias, sequencing error and varying tumour content from the tumour sample. Although there are a large number of tools available for analyzing somatic variation, choosing the right tool can be very difficult.
Here we present several examples of the testing and benchmarking of tools that have been done at the Genome Sciences Centre, and the process that we used to select a tool for our analysis pipelines.
We will also present a somatic variant data set which we constructed based on the sequencing of a metastatic melanoma cell line, COLO-829 and its matched normal. With these results, we were able to generate a somatic reference standard for cancer genome sequencing and benchmark a number of somatic variant callers.
This seminar is for anyone interested in learning more about ways to test and benchmark tools for analysis of whole genome and transcriptome sequencing data. No prior knowledge or experience is necessary. This will be an information-sharing session.