How to filter out contamination at samples

Dear all,

I am processing our sequencing data and I have a problem. There are a lot of observed features at kitom (water processed by the kit for DNA extraction) and negative controls. I am wondering if there is some possibility to filter out these features? I mean like background?

I know there are some commands for filtering (Filtering, taxonomy, and phylogeny - Microbiome Analysis with QIIME2), but these are not ideal for my purpose.

Thank you very much!

Martin

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:

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

3 Likes