@PartridgeCG Low DNA quantity CAN be an issue, but if you get enough DNA to make a library, I'd probably recommend metagenomics.
But don't take my word for it alone!
@PartridgeCG I mean, you can definitely run functional gene analysis/pathway analysis and see what you find.
lots of thoughts on this, and I can selfishly point to tools I've worked on to process, but that's mostly bells and whistles after you make a decision.
@PartridgeCG Downsides to metagenomics:
Sensitivity: If you have the potential for lots of host DNA, it can be a problem (imagine 50 mouse reads for every bacterial read)
@PartridgeCG Reasons I recommend shotgun metagenomics:
1) Analysis is simplified
2) Library prep is WAAAY easier
3) Lower bias (still an issue from lysis, etc)
Cost: If you're having to pay for a whole flow-cell to run 16S, it likely is more expensive to do 16S until you have > 96 samples
@WhySharksMatter Is there a gritty reboot of "West Side Story", where the Sharks are on coke, and the Jets do meth, and the journalists are just confused?
@mtanichthys @PartridgeCG It's only useful if you have a computer with more than 4 cores, really. If you do, though, it's almost always faster and easier than for loops.
@michaelhoffman If you can't figure out how to do something in a particular language, it is obviously the fault of the language, and you should go ahead and learn another one.
Related, the speed of the interpreter is far more important than the portability of the code...