Hi community!!! This is my first post and I am very new in this field and naive with MEGAN.
I am analysing already submitted shotgun WGS metagenome sequence data with MetaPhlAn software. Can anyone please tell me if I can use MEGAN for rarefaction analysis of the shotgun sequence data?
If yes, then when I have to do the analysis-
1.prior to MetaPhlAn run? or,
2.after the bowtie2 step of MetaPhlAn? or,
3.after the profiling step of MetaPhlAn?
Thanks and regards,