Hello, I ran 2 different types of binners on 12 assembled metagenome samples, one was metabat2 and the other was vamb. I ran CheckM and GTDB-Tk on both the metabat2-produced bins and the vamb-produced bins, and got similar but slightly different results. When I report my results, which binner results should I focus on? Metabat2 generally produced a higher number of bins, but some of them are lower quality than the vamb-produced bins. For taxonomic information, there were some differences in microbe identity. There were microbes that showed up in the GTDB-Tk results for both metabat2 and vamb, but a few microbes showed up from the metabat2 bins but not the vamb bins (and vice versa). I'm not sure which results to use, or if I should report both. Is it better to have a higher number of bins produced, or a lower number of bins but with higher completeness? How should I handle the differences in taxonomic assignments? Any guidance would be useful, thanks.
