Metadata connections SQMtools

[inej90]

Dear Fernando,

I obtained tables running the SQM using Flye coassembly. On other hand, I have created a metadata table where I have all the information about my samples.

My question is: how can I connect tables generated by SQM and my metadata to visualize diffrences for example between farms, animal pruction system etc...? Can I obtain taxonomic results by farm instead of identification number (which I put at the beginning of the SQM analysis in my file samples) or not?

Thank you in advance.

[fpusan]

See the parameter metadata_groups in plotTaxonomy, It may do what you need.
But generally speaking SQMtools will not handle metadata, and you will need to manually pass the right information to whichever R package you are going to use for downstream analysis.

I may consider writing a wrapper that goes from SQMtools (plus an optional metadata table) to phyloseq, which would be useful since phyloseq does handle metadata.