Hi bioBakery crew,
I’ve been running some tests with Metaphlan to profile marine metagenomes, but the tests return 0 hits (e.g. profiled_metagenome.txt: UNKNOWN -1 100.0). It thus seems obvious to conclude that the marker genes DB doesn’t properly cover marine microbiomes. Is that correct?
Also, I recently built a large plankton-specific DB (UniRef90 annotations) which has proven quite effective at profiling plankton communities using Humann 3.0. This DB was previously clustered using Linclust. The question that arises now is: how would you extract marker genes from such a customized DB in order to expand the Chocophlan DB used by Metaphlan?
Any input would be greatly appreciated!