Exporting qiime2 biom files with metadata?


I am trying to export a .biom file to eventually convert to . tsv file to use LEfSe on (https://huttenhower.sph.harvard.edu/galaxy/). I am able to do this just fine, but I am unable to get a file with the one line of metadata I am interested in actually feeding this program to be included (in my case, the sex of the person that each sample came from).

How does one export a .biom file with metadata included from qiime2? I’ve tried to add the meta data to the .biom file with a .tsv file, but it never actually adds (referencing Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)). Can anyone provide any help?

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You can try to add the meta-data on your own, as long as you match it with the correct sample:


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Thanks for the reply. Do you mean open the file and actually add the data? I could but it’s a lot a lot of samples. Do you know of a simpler way?

Hi @ben and @msport469,

Im going to bump this over to the "other tools" category, since it deals with biom-specifically and not a QIIME2 plug in, but also maybe look at this, it at least specifies export with metadata.

Or, if you're so inclined, the python API isn't bad for this.