Niklaus Grunwald

@grunwald.bsky.social

887 Followers 698 Following

Genomic epidemiology, population genomics, plant pathology, pathogen emergence, #Oomycetes, #Phytophthora, #SuddenOakDeath. Opinions are my own. 🧬🦠🧪🖥️

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.

Condensed phylogenetic tree inferred from a 134-taxon, six-locus nuclear alignment (LSU, btub, tef1a, hsp90, rpl10 and enl) showing the relationships between the #Phytophthora clades and DM groups (redrawn from Bourret et al. 2018). Groups or taxa with an obligate biotrophic life-style are highlighted in green.

The global survey indicated that people have moderately high levels of trust in scientists overall.Credit: Michael Candelori/Pacific Press Via Zuma Wire/Shutterstock