Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads.

ABSTRACT:

Background

Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads.

Results

We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford

SUBMITTER: Commichaux S 

PROVIDER: S-EPMC8157722 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature