PRE-MEETING WORKSHOP: Automated analysis of pathogen genomes using PathogenSurveillance and the genomeRxiv web server

Ticketed event; preregistration required

Description: Generation and analysis of whole genome sequence data remains challenging. However, new computational technologies are rapidly making whole genome sequence analysis more accessible. In this workshop, participants will learn how to work with the nf-core pipeline PathogenSurveillance (PS) and the genomeRxiv web server. PS is a population genomic pipeline for pathogen diagnosis, variant detection, and biosurveillance. The pipeline accepts short and long read data. Significant features include the ability to analyze unidentified eukaryotic and prokaryotic samples, creation of reports for multiple user-defined groupings of samples, automated discovery and downloading of reference assemblies from NCBI RefSeq, and rapid initial identification based on k-mer sketches followed by a more robust core genome phylogeny and SNP-based phylogeny. The genomeRxiv web server provides a powerful method to infer the identities of fungal and bacterial pathogens at within-species resolution either using assembled genomes or k-mer sketches of unassembled genomes as queries. genomeRxiv and PS can be used in parallel to automate genome processing and analyses. Together these two approaches simplify and accelerate use of genome sequencing in disease diagnosis by returning multiple outputs to cross-validate pathogen identification. They also accelerate whole genome data processing and analyses for use in fundamental research. Participants are expected to bring their own laptop, and all computational work will be done in a virtual learning lab on gitpod.

Plant Health 2025 Theme: Plant pathogens continue to emerge at accelerated rates globally due to increases in trade, climate warming and land use. Rapid tools for biosurveillance of pathogens that can diagnose pathogens in real time, detect new invasive species and novel variants are needed to address Global Risk.

Target Audience: This workshop is geared to graduate students, postdocs or scientists that want to analyze whole genome sequences for pathogens including bacteria and eukaryotes (but excluding virus genomes).