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Metaphlan2 and Kraken2 gives very different results

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.

Hi,
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