Merge Metaphlan output

Is there a way to merge the metaphlan outputs from multiple different samples so that I can have their data combined as one treatment group rather than individually?

Hi @bethp

Do you mean grouping the files into a collection? Then, yes.

Trying running all of your samples though together. You can tag the inputs with tags for the samples and the treatment groups.

Then, you can combine some of those intermediate outputs (SAM, etc) but maybe not all… I have never merged a BIOM file but maybe others have and can comment about that. Collapse samples seems to do the reverse, and is part of the QIMME package, so presumably some tool outputs a multi-sample BIOM.

Could you clarify what you are trying to do if this is not enough? We could bring in some metagenomics experts for more help, and they will appreciate some context.

Thank you! I’d like to be able combine the abundances from Metaphlan by group and visualize these using Krona or another visualization tool.

So what you’re saying is I still should run all of my individual samples through Metaphlan, tag them with their group, then combine the outputs for each group into their own collection, and then use that collection for visualization? For example in krona then, I can select the “Combine data from multiple datasets?”

Yes :slight_smile: Please give this a try

Thanks! I was able to combine the datasets for Krona. As a follow-up, is there a way to merge/combine the relative abundance tables from Metaphlan in Galaxy so that I can compare multiple samples’ abundances side by side and see the species that are common among these samples?

I found the “Merge” tool to do this in the EU Galaxy but not in the US Galaxy. However, open to suggestions on other ways to accomplish this

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Hi @bethp

If you post back the full tool name/version of the tool that is only at the EU server, we can see about adding it to the ORG server :slight_smile:

Thanks! It is the Merge_Metaphlan_tables tool

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Great, thank you @bethp

The ticket is here for the installation request. You can follow this for updates. Install humann_join_tables/3.8+galaxy0 at ORG · Issue #713 · galaxyproject/usegalaxy-tools · GitHub

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