Compute core microbiome

Is there a compute_core_microbiome.py equivalent for QIIME 2? A search didn’t turn up anything. It was great to use in QIIME 1. Thanks!

Hi @CarlyRae! Have you seen feature-table core-features? I think this is the Q2 equivalent of that Q1 script. Keep us posted! :t_rex:

Perfect. That looks like the equivalent! Thanks

Follow up question: previous command in QIIME 1 could run this from the tutorial website http://qiime.org/scripts/compute_core_microbiome.html

Identify the core OTUs in otu_table.biom, defined as the OTUs that are present in all of the samples in the ‘Fast’ treatment (as specified in the mapping file). Write the list of core OTUs to a text file.

compute_core_microbiome.py -i otu_table.biom -o otu_table_core_fast --mapping_fp map.txt --valid_states “Treatment:Fast”

I don’t see an equivalent in core-features. Is there a way to specify mapping file categories to look at?

Hi @CarlyRae,

This sounds like a handy option to have! Not sure if that is directly available using the core-features function yet. While you wait for one of the expert’s to confirm that, I can suggest a couple of alternative (though not very graceful) ways to get what you want.

You can create a new feature table with only the samples from the treatment group of interest using the feature-table filter-samples function as shown in this tutorial here. Once you have that new feature table you can simply run the core features function with whatever fraction setting you need on the new table.

Alternatively, if you are more comfortable with the qiime1 workflow for this option, you can export your biom table and carry out those commands in qiime1. The downside to this is if you decide to re-import anything back to qiime2 they will be missing the previous provenance attached to them.

Hope that helps!

1 Like

Thanks @Mehrbod_Estaki - I think your approach is consistent with what I would recommend in this case. @CarlyRae, you could also group your feature table using your metadata - YMMV. Let us know how that works out for you! :t_rex:

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.