I have reads generated from taking a fecal sample and then performing NDA to amplify the DNA. We used a serial dilution method to attempt to isolate a single bacterium from this sample. I am trying to determine if we can computationally confirm only a single bacterium is in this sample.
My current rough idea is;
Use QIIME to determine if the sample contains OTUs from more than one species (using de novo OTU selection.) If only one species of OTUs exist, use SPAdes to generate a de novo assembly. Using this assembly map the reads back on to the scaffold and perform variant calling. If any SNP exists at a coverage above a certain threshold, conclude that the given variant must be from having two organisms pooled together.
Is this possible or are these methods inherently too unspecific to be able to perform this analysis with any sort of certainty?
Is there another way to do this that I have not thought of?