strange resultes to me

[mengyuan-JI]

Hi, May i ask you something regarding the methods dRep use.
When I run "dRep dereplicate ./dRep_3test/ -p 20 -g ../ALL_MAG/.fa --genomeInfo ./MAG_info_for_dRep.csv" for 2300 genomes , I only get around 246 represent genome, while "dRep dereplicate ./dRep_5test/ -p 20 -comp 50 -con 10 -sa 0.95 -nc 0.5 -g ../ALL_MAG/.fa --genomeInfo ./MAG_info_for_dRep.csv" give me 430 genomes , it is very strange to me, since the seconde command should filter more input gennomes and it looks more strictly. but get more resulted genomes.
Thanks for your consideration

[MrOlm]

Hi @mengyuan-JI - I think the discrepancy is due to the -nc 0.5 argument. See here for why: https://drep.readthedocs.io/en/latest/choosing_parameters.html#minimum-alignment-coverage

Best,
Matt