How to filter out contamination at samples

[jwdebelius (Justine Debelius)]

Hi @Martin1,

The short answer is yes, but not in QIIME 2. The longer answer is that it's complicated and depends on the biomass of your sample, whether you used robotic extraction, and what sequencer you used, among other factors.

You might look at this thread and linked threads:

Discussion: methods for removing contaminants and cross-talk

Thanks for the report @lewisNU! I have not tried this method yet, or heard any reports on the forum from others who have given independent tests of it, so it is very good to hear your results. Just to be clear: decontam is not yet incorporated in QIIME 2 and is not associated with the core development team. I am excited to try this method out and incorporate it into when I can — and am very excited to hear about what others are doing for contaminant detection and removal. W…

You might also want to explore some of the additional literature

Well to well contamination:
https://journals.asm.org/doi/full/10.1128/mSystems.00186-19

Low biomass filtering

https://journals.asm.org/doi/full/10.1128/mSystems.00163-18

You may also want to look for Amy Willis's new preprint with Nearing and Callahan (I dont remember the name, I'm sorry!). She's doing some innovative things.

Best,
Justine