Problems Creating a Compatible Open Reference OTU Table for PICRUSt


I am trying to create an OTU table that I can input into PICRUSt. The table is an open reference table, and according to the PICRUSt tutorial page that is okay. However the tutorial page informs users to do the following steps to make it compatible for PICRUSt:

Using an open reference OTU table from QIIME

  • You may have already picked OTUs using an ‘open reference’ approach and don’t want to have to re-pick OTUs just for PICRUSt. That is ok, but you have to first remove the de-novo OTUs by keeping only those OTUs that have matching greengene ids.

*To make your open reference picked OTU compatible with PICRUSt: -i otu_table.biom -o closed_otu_table.biom --negate_ids_to_exclude -e $PWD/gg_13_5_otus/rep_set/97_otus.fasta

I was informed this script is for QIIME not QIIME2.
From what I have seen, QIIME2 is using “plugins” rather than “scripts”, but I cannot find a plugin that could be used for this same function. Is there a plugin that could be used instead for QIIME2?

Any advice would be greatly appreciated. Thanks.

:pie: :pie: :point_down:

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