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WORKSHOP: Detection of plant pathogens in metagenomic sequence data using Microbe Finder (MiFi®)​​

​Broadcast Date: Tuesday, November 16, 2021 | 11:00 AM –​ 3:00 PM US Central Time​​

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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.​

Learning Objectives

  • Hour 1&2 – principles of developing, curating e-probes for plant disease diagnostics with High Throughput Sequencing data- hands on tutorial. 

    • ​After attending​​ this workshop, attendees who develop plant pathogen diagnostic assays and tests, will be able to add HTS data management to their toolbox. They will come away with a better understanding of what diagnostic assay validation means, and how to apply it to HTS data. 
  • Hour 3&4 - principles of e-probe validation and performance characteristics for plant disease diagnostics. 
    • ​​​The attendee will have developed and curated an e-probe set for a pathogen of their choice, and learned about the wet lab techniques to validate and test the probes. 

  • Hour 4 - principles of e-probe usage for plant disease diagnostics with sequence data – hands on tutorial. 
    • ​​​​​The attendee, will learn how to use the e-probes in the MiFi website and get to know what probe sets are already available for use by diagnosticians and researchers.​

Target Audience

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 University​
Yazmin Rivera, USDA-APHIS-PPQ-Science and Technology
Martha M. Malapi-Wight, USDA-APHIS Plant Germplasm Quarantine Program​ 


Andres Espindola, Oklahoma State University​