Softwares for statistitical analysis of MetaPhlAn output

Question

[dpc]

Hi community!!! I have profiled shotgun metagenome data with MetaPhlAn. Now, I want to do statistical analysis (e.g. alpha-, beta- diversity comparison, rarefaction graph, boxplots, PCOA, etc) with the output data. Can anyone please suggest me which software can I use? (provided, I don’t know language like R, python, etc.)

Thanks and regards, DC7

Answer 1

[antonioggsousa]

Hi,

You might want to try to use STAMP: Statistical analysis of taxonomic and functional profiles.

It is the only GUI software that I know that may help to perform statistical analyses on taxonomic and functional data tables.

Please read the user guide first to see if the software does what you want.

I hope this helps,

António

P.S.: I never use MetaPhlAn, so I don't know which type of output generates and if STAMP can handle this or not.

[dpc]

Thanks sir. It can import MetaPhlAn output. But I'm getting error like this:

classification: k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales_unclassified|g__Gemella

error: "Child g__Gemella has an unclassified parent."

Any idea?

[antonioggsousa]

Hi,

Not sure. From the error it seems related with the fact that for that particular taxonomic annotation you got something annotated at genus level - g__Gemella -, but not annotated at family level f__Bacillales_unclassified, that is a higher rank just above the genus. This is quite strange, because if you know what is the genus, you should know the family.

I think the program is complaining about that. I guess this is related with the taxonomic database that you've used. Was this database the database recommend by MetaPhlAn? If so I suggest you to contact the developers of MetaPhlAn to try to address this issue.

António

[dpc]

Yes sir. The database is CHOCOPHLAN v30 which is recommended by MetPhlAn3. I have created a thread regarding this problem in the metaphlan forum as well as in biostars. Thanks