Updating pre-existing catalog and functional profiling

[sarpiens]

Hi, I had a couple of questions regarding the pipeline and the generated catalogues:

• I was wondering, if you could guide me through the process of updating a pre-existing catalogue. This is something I've seen you mention in the release, but I haven't seen it documented in the github.

• I was wondering which of the generated catalogue files would be used to make a functional metagenome profile and which program could I use (Humann3, etc)?

Thank you very much in advance. Best regards, Sam

[tgurbich]

Hi Sam,

The update process is described in the methods section of the MGnify Genomes publication here. We don't yet have a public pipeline for this but it is coming within a year or so.

As for the functional metagenome profile, I am afraid it is too broad of a question for us to advise you on. It probably wouldn't make sense to do it for a catalogue since it is a collection of many samples. Generally speaking, tools like Humann3 and DRAM can be used for this but the inputs would depend on your goals.

Best wishes, Tanya

[sarpiens]

Hi Tanya. Thanks for your feedback. As for the functional metagenome profile, mi question was which files of the produced catalog could be used as reference files for a typical functional profiler. I have seen that the pipeline already generates kraken+bracken databases that could be used for taxonomic profiling of metagenomes, but is not clear to my which files could be used as reference for functional profiling of metagenomes, if any. Best regards, Sam

[tgurbich]

Hi Sam,

We describe all files available as part of the catalogue in the associated README file on our FTP. For example, here is the file for the human gut catalogue. I would suggest checking these to see what files, if any, would be appropriate for the tool you would like to use.

Best wishes, Tanya