Hi Stephen,
Thanks for the great tool. I have a set of species-level MAGs that range in completeness from 50-100% and redundancy/contamination 0-10%. These are species representatives chosen using dRep with a genome average ANI cutoff of 95%
Since these are environmental MAGs, I would like to construct my own database. Given the above numbers, can I include all MAGs or is it better to include only MAGs that are substantially complete say >70%? Also, to what extent does redundancy affect downstream steps such as calling SNPs?
Hi Stephen, Thanks for the great tool. I have a set of species-level MAGs that range in completeness from 50-100% and redundancy/contamination 0-10%. These are species representatives chosen using dRep with a genome average ANI cutoff of 95%
Since these are environmental MAGs, I would like to construct my own database. Given the above numbers, can I include all MAGs or is it better to include only MAGs that are substantially complete say >70%? Also, to what extent does redundancy affect downstream steps such as calling SNPs?
Best, Adi