Hi! I found this other related post (Is Humann3 comparable with Metaphlan4.0.6? - #6 by strainliu) where you say that as max_taxonomic_profile is not widely used it has not been updated. In the post they refer to humann3.7 and metaphlan4.0.6 compatibility, I wonder if this has been updated for humann3.8? From what I’ve been seeing the biggest bottleneck is usually the indexing of the database with bowtie2 build, so this option is very interesting when I have a lot of samples to process.
On the other hand, I wanted to ask whether this option could be dangerous. For example, a decrease in the precision of the results stratified by species, i.e. if there is a higher risk of false positives (detecting species that are not in the sample) if the index is used based on the whole dataset instead of each of the samples?
Thanks in advance. Sam