I ran one sample through Metaphlan2 and kraken2 for classification. But the results from Metaphlan2 and Kraken2 is completely different. I am not sure which one I have to rely? Any insight would be greatly appreciated
me too. This problem confounded me a lot.
sorry for the delay and not catching up the post earlier.
See this response on the GitHub issue tracker https://github.com/biobakery/MetaPhlAn/issues/90