Multi-gene amplicon sequences with dada2

[ebolyen (Evan Bolyen)]

@Stream_biofilm

Would I be able to do this using the dada2 R package and then transfer the files back into qiime2?

@benjjneb

I also wonder if one of the Q2 masters might know if a method that can do this is already included in Q2?

I wrote a post for importing your data after following the DADA2 tutorial. Getting the FeatureData[Sequence] artifact is pretty easy, but the FeatureTable[Frequency] takes a bit of massaging.

@benjjneb

The algorithm should easily separate the different gene regions from each other.

That is super cool!

@Stream_biofilm

Also, would there be an issue on running dada2 with multiple genes not parsed and then separating them downstream?

I can't think of a good way to separate them after the fact in QIIME 2. So splitting them, then using DADA2 directly (with matchIDs=TRUE) may be your best option.

In the future we might be able to frame this problem as removing "contamination" (@Nicholas_Bokulich is working/thinking about plugins for that), but I couldn't say for sure.