A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.

ABSTRACT: The Centers for Disease Control and Prevention's national tick and tick-borne pathogen surveillance program collects information to better understand the regional distribution, prevalence, and exposure risk of host-seeking medically important ticks in the United States. A recently developed next generation sequencing (NGS) targeted multiplex PCR amplicon sequencing (MPAS) assay has enhanced the detection capabilities for Ixodes-associated human pathogens found in Ixodes scapularis and Ixodes pacificus ticks compared to the routinely used real-time PCR assay. To operationalize the MPAS assay for the large number of tick surveillance submissions processed each year, a reproducible high throughput bioinformatics pipeline is needed. We describe the development and validation of the MPAS pipeli

SUBMITTER: Osikowicz LM 

PROVIDER: S-EPMC10878300 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature