New module

[SilasK]

Question from @JoseLopezArcondo

Dear Silas,

I would like to include motility as a "module", is there a way to include this, maybe from your jupyter notebook?

Best

Do you have a clear idea of what "motility" means? e.g. do you have a list of KO that would make up a module for "motility" ?

If you have a set of KOs (or other annotations) you could try to create your own module.

I did this for SCFA in this notebook. I assume in your case it would be rather a set of genes than a "path".

Eventually, it would also be cool to include it in DRAM. but this would take some time until it's validated.

An alternative would be https://github.com/hzi-bifo/traitar

[JoseLopezArcondo]

Hello Silas, well the fastest one would be I guess I would include all KO functions with the "flagella" word in it here
https://raw.githubusercontent.com/shafferm/DRAM/master/data/genome_summary_form.tsv
But I am not sure if there are redundant functions there or how to check this, to eventually calculate completeness in a reasonable way...
best
josé

[JoseLopezArcondo]

Another question I have is, are modules included in ATLAS from DRAM redundant to some extent with those from DRAM itself? Are product categories from DRAM also present in ATLAS modules?

[SilasK]

I use dram 1.4 to annotate genomes. So you get everything from dram with atlas.
What I do in addition, is to distil/aggregate all kegg modules. I think this is not included in the default dram output. but the definitions are from the dram team..

[SilasK]

Here is a example output of dram 1.3 within atlas https://github.com/metagenome-atlas/Tutorial/tree/master/Example/genomes/annotations/dram

[JoseLopezArcondo]

Thanks, so results in kegg_modules.tsv should not include some metabolisms in distill/products.tsv then? or there's some possibility of redundance?

[SilasK]

The products.tsv from dram is a selection of most important pathways that are also displayed in the html report. I took the same code end run it on all kegg_modules (defined by dram). So there is an overlap.

[JoseLopezArcondo]

Thanks, So DRAM products have names and do not mention the module id then, right?
And are CAZy also included in kegg_modules?

[SilasK]

No CAZy are not included in kegg modules