Q: Which is better for taxonomic classification of #metagenomics samples - Kraken2 or MetaPhlAn 3?

A: It really depends!

Read the very short story in this thread, or the full story in my preprint w/ @BetaScience and André Comeau: bit.ly/3EWkYJf

1/ Now, you may be thinking "but aren't there loads of studies that compare different metagenomic taxonomic classifiers already?" (& you would be right), but what they don't do is compare the impact of different parameters and reference databases on the classifications.

2/