MMID Bioinformatics Workshop - 2023-03-23 Introduction to Bacterial genomics

INSTRUCTOR
Jill Rumore
Biologist / Ph.D. candidate
Surveillance, Outbreak Detection and Response, Division of Enterics, Public Health Agency of Canada
Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba

BACKGROUND
Jill has been a Biologist with the Public Health Agency of Canada since 2014 and is in her 4th year of Ph.D. studies at the University of Manitoba in the Department of Medical Microbiology and Infectious Diseases. She is supervised by Drs. Natalie Knox and Celine Nadon and her research project is focused on developing an end-to-end metagenomics-based pipeline for rapid detection of bacterial foodborne pathogens in foods and clinical specimens. She routinely works in conda to conduct her research and has considerable experience with computer coding languages BASH and R.

WORKSHOP
This workshop will provide demonstrations and exercises for performing basic bioinformatics analysis of bacterial genomic data as it pertains to quality control and data preprocessing, which are critical to obtaining high-quality data for downstream data analysis. Specifically, we will assess general data quality using FastQC, filter low quality reads using fastp and remove host sequence content using a combination of Bowtie 2 and samtools. We will also explore the use of checkM to assess the completeness and contamination of bacterial genome assemblies.

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Workshop materials are available in our GitHub page:
2023-03-23-Bacterial-Genomics

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For more information on our workshop, please visit our website at:

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MMID Bioinformatics Workshop Series aims to teach basic coding languages BASH and R to empower participants with the freedom and flexibility to manage their own datasets.