Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance.

ABSTRACT:

Background

As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validatio

SUBMITTER: Timme RE 

PROVIDER: S-EPMC5782805 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature