Would SeqSNP work on pathogen detection from environmental water samples?

Unfortunately, as this is a diagnostic request, this is a project we would not be able to support. Also, the limiting factor would be the concentration of the target organisms. A process of filtration/concentration would need to be performed, and/or an amplification/culture step. By introducing amplification steps (e.g. pre-amplification PCR or a nested-PCR), bias may be introduced in terms of proportion of each target. In addition, culturing would only work on bacterial species, and would not be applicable for non-cultivable organisms (e.g. certain species of parasites and viruses).