Is decontam available in QIIME 2?


(Tomas Eagan) #1

Dea Nicholas, any updates on including a decontam plugin in qiime?
(struggling with R right now…)


(Nicholas Bokulich) made this topic public #2

(Nicholas Bokulich) #3

Not yet but maybe soon. The authors very understandably did not want to add a decontam method to QIIME 2 until their work was published, which it now is as of December 2018. :tada:

cc: @benjjneb


(Ben Callahan) #4

Yes I’d be able to help add decontam to Q2 at some point now that it is published.
Is there a GH issue on this open yet somewhere?


(Nicholas Bokulich) #5

Not yet.

We had discussed adding this to q2-quality-control once upon a time — it is your call whether to add this to that plugin or create a new plugin (q2-decontam?) to house this method.


(Ben Callahan) #6

Does the action of decontam, which identifies contaminants after initial processing QC into ASV/OTU/taxa tables, fit with the functionality in q2-quality-control?

If decontam is added to q2-quality-control, does the provenance mechanism in Q2 note the decontam method and guide users towards how to cite it? Or does that just happen at the plugin level hence would need its own plugin to be easily discoverable/citable via provenance?


(Nicholas Bokulich) #7

q2-quality-control is a bit of a hodge podge right now. I would say yes, it fits the original intent of q2-quality-control for filtering and evaluation of data post-processing (though that intended role has yet to fully manifest itself, and lots of stuff in there is more evaluation tools). The other post-processing QC type method in there right now is positive + negative filtering based on alignment.

Yes! Citations can be defined both at the plugin level (e.g., this) and the action level (e.g., this). Those citations will be recorded in provenance and hence be discoverable to users.


(Ben Callahan) #8

That seems reasonable. I would prefer to not create a new plugin, simply for reasons of keeping my maintenance burden limited and focused on just one primary outlet (the R packages).


(system) closed #9

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