A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes.

ABSTRACT: Cyclospora cayetanensis is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challenge. To address this issue, development of new methods based on potential genomically-derived markers for strain-level identification has been a priority for the food safety research community. The absence of reference genomes to identify nucleotide and structural variants with a high degree of confidence has limited the application of using sequencing data for source tracking during outbreak investigations. In this work, we determined the quality of a high resolution, curated, public mito

SUBMITTER: Gopinath GR 

PROVIDER: S-EPMC5891936 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature