Question about genomes dereplicated by dRep and multigroups MAGs METABOLIC-C analysis

[LvbBo]

Dear author:
Your paper mentioned that: First, all the microbial genomes were dereplicated by dRep v2.0.5 [54] to pick the representative genomes for downstream analysis using the setting of “-comp 85.”Here, I want to know if “the setting of -comp 85” is mandatory? Can I set -comp 50? Will it affect the quality of results?
Second, I want to know how you conduct multiple comparisons? I have multiple water samples (from the same sea area), which are divided into four groups (four water layers), and each group contains different samples (over 60). Under such circumstances, how should I use this software (METABOLIC-C)? Should I run it four times for the four groups? In the issues/116, you mentioned "Hi, yes, you can run the analysis for seven times for MAGs and reads from individual samples, and then get the average genome coverage for each group. Or a possible but energy-consuming alternative is that you can re-assemble group A and B reads and perform MAG reconstruction for these two groups. The seven sets of reads will be re-assigned to the group A and group B communities separately. This way, you will treat group A and group B datasets as two individual samples, and only need to run two times of METABOLIC-C." I'm not sure how to implement your method, it is hard for me. Therefore, could you tell me another solution? Looking forward to your reply!!! Thanks!