Bioinformatics School: Building a Skilled Workforce in Infectious Disease Epidemiology

More critical now given the COVID-19 global pandemic, bioinformatics skills are urgently needed to support rapid translation of infectious disease research to improve healthcare and decision making. This need is further compounded by the surge in genomic and epidemiological data being generated globally by researchers. Public health infectious disease researchers and practitioners are increasingly seeking computational skills to aid their analysis, comprehension and research translation activities. However, acquiring this level of topic specific and advanced bioinformatics knowledge and skills is challenging because adequate training programs are scarce. The Canadian Bioinformatics Workshops proposal herein seeks CIHR funding to redevelop its 'Infectious Disease Epidemiology' workshop and to provide accessible training opportunities to Canadians for immediate skill development in the cutting-edge bioinformatics resources and tools necessary for pathogen research. The updated 'Infectious Disease Epidemiology' workshop will be an intensive 4-day, virtual hands-on workshop designed to guide researchers through the key bioinformatics concepts and tools required to analyze pathogen genomic data sets and integrate epidemiological data. Participants will gain practical experience and skills to be able to: 1) understand next generation sequencing (NGS) platforms as applied to pathogen genomics and metagenomics sequencing; 2) analyze NGS data for pathogen surveillance and outbreak investigations; 3) identify and analyze antimicrobial resistance genes; 4) detect emerging pathogens from metagenomics datasets; 5) perform phylodynamic analysis on these datasets; and 6) use visualization tools for genomic epidemiology analysis. Becoming proficient in these computational skills not only has direct and immediate impact on current public health pandemic efforts, but also engages and accelerates new infectious disease research for the long-term benefit of public health in Canada.