Hi there! I am also looking for recommendations for "selecting" mags for downstream analyses: there are multiple assemblers and binners used by the pipeline and of course it will yield multiple copies of mags for from the same species. should I use taxonomy information get their identifications, then select the best one based on checkM2 results for the same species? Could I select mags from different assemblers and binners? For example, can I select the mag from MEGAHIT_MaxBin2 for species 1, and SPAdes_SemiBin2 for species 2? Thanks!

Hi @Ruiqi Li. You can run dereplication, either with dRep or skder to select a representative collection of bins. We plan to integate this step in mag too in the future.

Great! Thank you!