Discussion: methods for removing contaminants and cross-talk

[Nicholas_Bokulich]

@lewisNU

I’ve previously used decontam prior to it being incorporated into QIIME 2, and whilst I’m a huge fan of the principles it’s built around, it didn’t work fantastically for my samples.

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 :qiime2: development team. I am excited to try this method out and incorporate it into :qiime2: when I can — and am very excited to hear about what others are doing for contaminant detection and removal.

@lewisNU

perhaps we are now nearing the stage where a very large round table is to be required to produce published consensus guidelines on how to deal with these anomalies.

We don't have a physical table, but this forum could be a great place to get that conversation started (it seems to be already — based on this conversation and earlier threads)

It could be really useful (in a new topic) to start this conversation and have folks share papers describing methods that they use for quality control. Ideally, we can form some consensus of community standards to recommend to others. Or, at the very least, we could work to incorporate a few of the top methods for QC/contaminant removal in :qiime2: so that we at least have better options that suit what our users need.