We would like to set up a method for rapid pathogen detection in a diagnostics lab. Since assembly-dependent methods are time-costly, we are looking for tools to give metagenomics the possibility to serve as diagnostic method.
An example of these kind of tools is this one:
Koslicki, David, Simon Foucart, and Gail Rosen. "WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification." PloS one 9.3 (2014): e91784.