make.biom with sample information

Hello All,

Would it be possible to add sample data support (e.g., experimental factor, sample collection date, etc) into the “make.biom” command?

Many thanks.

Could you post an example of what you would like the resulting biom file to look like?

Hi Sarah,

Mothur outputs this:

{“id”:“sample1”, “metadata”:null},
{“id”:“sample2”, “metadata”:null},
{“id”:“sample3”, “metadata”:null},
{“id”:“sample3”, “metadata”:null},

Could a “metadata” option be added (unless this is what the “groups” does), as in the example below?

{“id”:“sample1”, “metadata”:{
“Description”:“human gut”}},
{“id”:“sample2”, “metadata”:{
“Description”:“human gut”}},

The groups parameter is used to select samples you would like to include in the biom file. Currently we allow you to provide a *.contaxonomy file to fill metadata with the taxonomy information, but I think it would be fairly easy to add a metadata parameter to allow you to provide more generic data.

Maybe a metadata file like:

sample Tag1 Tag2 …
sampleName info info info …

For example:

sample site Description
sample1 “gut” “human gut”
sample2 “soil” “human gut”

Is that what you were thinking?

Hello Sarah,

Thanks for your reply. Yes, that is what I had in mind, a file with information to map samples to experimental parameters that can be passed as another option in the “make.biom” command.


This will be part of 1.28.0.

Great, thanks!