nf-core/pathogensurveillance is a population genomics pipeline for pathogen identification, variant detection, and biosurveillance. The pipeline accepts paths to raw reads for one or more organisms and creates reports in the form of an interactive HTML document. 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 multi gene phylogeny and SNP-based phylogeny.
Healthy plants are the foundation for life on our planet. They produce the oxygen we breathe and over 80% of the food we eat. The __Plantopia__ podcast series explains how protecting plant health can ensure a sustainable future. Inspired by the United Nations declaration of 2020 as the International Year of Plant Health, the American Phytopathological Society created Plantopia so you can explore the world of plant health in company with plant pathologists—people on a mission to protect plants and our food supply.