Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform.

ABSTRACT: Public health authorities whole-genome sequence thousands of isolates each month for microbial diagnostics and surveillance of pathogenic bacteria. The computational methods have not kept up with the deluge of data and the need for real-time results. We have therefore created a bioinformatics pipeline for rapid subtyping and continuous phylogenomic analysis of bacterial samples, suited for large-scale surveillance. The data is divided into sets by mapping to reference genomes, then consensus sequences are generated. Nucleotide based genetic distance is calculated between the sequences in each set, and isolates are clustered together at 10 single-nucleotide polymorphisms. Phylogenetic trees are inferred from the non-redundant sequences and the clustered isolates are added back. The method i

SUBMITTER: Szarvas J 

PROVIDER: S-EPMC7083913 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature