Marine Samples (Environmental samples) and disk space

Microbial community profiling HUMAnN
1

Hi team
I have almost finished my analysis (Marine water metagenome) using MetaphlAn3 and HuManN3.

I do need clarification

Can Metaphlan and humann be used for environmental samples (especially marine water)?

Both Kneaddata and humann produce temp life which occupies more disk space. Can I delete the files or do I have to keep them?

Thank you

2

Sorry to have missed this message before. MetaPhlAn and HUMAnN can be used on marine communities, however - as reference-based profiling methods - they may be more limited in what they can detect from that environment. The recently released MetaPhlAn 4.0 is expanded to include MAGs from marine environments, so it ought to perform better than MetaPhlAn 3.0 (or earlier) in that application.

You can delete the temp files when your jobs are done running. I recommend first saving the LOG file from the HUMAnN temp folder as it contains useful information, but most people would not use the rest of the temp.