LCA parameters for complex bacterial communities

Hello everyone,

I’m working with shotgun metagenomics data from natural bacterioplankton assemblages. I’m trying to figure out the optimal LCA parameters when applying daa-meganizer to this kind of complex bacterial communities. I’ve been reading through the literature and found different combinations, but I wonder if Megan (community) has any strong suggestion considering this kind of bacterial communities.

Many thanks in advance.