Broadcast Date: Tuesday, November 16, 2021 | 11:00 AM – 3:00 PM US Central Time
View On-Demand Workshop
The purpose of this workshop is to expose plant pathologists and stakeholders to the use of shotgun metagenomic sequencing and MiFi® for the simultaneous detection of viral, bacterial and fungal plant pathogens. MiFi® is a user-friendly graphical user interface (GUI) that was developed by scientists at the Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University. The GUI is a bioinformatic pipeline containing carefully designed databases of unique sequences of targeted pathogens called e-probes. Short and long read HTS-data can be used with MiFi®. The workshop will include the design and curation of e-probes (MiProbe) as well as the use of the e-probes in diagnostic settings (MiDetect). The e-probe design will include knowledge on how to select inclusivity and exclusivity panels, retrieval of genomes, development of raw e-probes, e-probe curation and calculation of diagnostic sensitivity, specificity and limit of detection based on simulated HTS data. The second part of the workshop will use metagenomic (HTS data) to learn how e-probes are used by diagnosticians (MiDetect). HTS data will be provided, alternatively, the participants can bring their own data. Funding sought only for in-person workshop.
Diagnostic laboratories that can include, but are not limited to NPDN, NCPN, private diagnostic laboratories and researchers interested in developing e-probes to increase MiFi’s detection capacity.
Kitty F. Cardwell,
Oklahoma State UniversityYazmin Rivera, USDA-APHIS-PPQ-Science and TechnologyMartha M. Malapi-Wight, USDA-APHIS Plant Germplasm Quarantine Program
Andres Espindola, Oklahoma State University