Bioinformatic analysis of metagenomic sequence data has been a bottleneck for diagnostic analysis. Most available tools require that the user have computer coding skills and access to high throughput computing. Taxa assignments using bioinformatic tools often lack enough resolution to detect microbes at the species/strain level. Microbe Finder (MiFi) is a web application that allows microbial community detection at species and strain level resolution without the need of coding skills. Obtaining metagenomic sequence data, from both host tissue and resident pathogens, is cheaper and easier. Ability to simultaneously screen for all possible pathogens in a single sample will enable more timely response, mitigation and management of potential plant disease introductions and outbreaks. MiFi relies on the successful development and validation of unique signature sequences (e-probes) for targeted query of metagenomic sequence databases for pathogen detection. Whole genome sequencing (WGS) coupled with targeted detection such as with MiFi e-probes has promise to overcome some of the technical difficulties in detection of and/or declaring freedom from a set of pathogens in a sample. Until recently, WGS has been constrained by cost, data volume, and limited bioinformatic tools for analysis, creating a bottleneck to adoption by most diagnostic clinics. With decreasing sequencing costs and bioinformatic tools like MiFi, the constraints are resolved. Here we introduce MiFi as a tool for plant pathologists that want to develop and use it for their research and daily diagnostics.