Basically, MAGs are bins that have been checked for completeness and refined if necessary. Any of your bins that are >90% complete and <10% contaminated can be considered MAGs as they are. Some people will even say >70% complete and <10% contaminated already qualifies as a MAG.
Yet if your bin is only 30% complete, or maybe 100% complete but 300% contaminated, you will have to work on them before they can be considered MAGs.
Well, it is always advisable to check the bin quality before declaring it as MAG.
Usually, after binning, I try and assess its quality using checkM, along with some additional parameters such as the number of predicted genes per bin, assembly size, coverage, GC content, and etc. Also, I predict the organism-specific phylogenetic markers such as 16S rRNA or ITS and then search them in the database to check whether the predicted bins have any contamination OR not.
Thank you very for the help!!!
Hello Mensur, do you have any cite of this so I can add it to my thesis references?
Thanks for this answer
The following paper explains some of the topics we discussed:
thanks so much.