# Metaphlan2 and Kraken2 gives very different results

**URL:** <https://forum.biobakery.org/t/metaphlan2-and-kraken2-gives-very-different-results/698>\
**Category:** MetaPhlAn\
**Created:** [July 9, 2020, 8:36pm UTC](https://forum.biobakery.org/t/metaphlan2-and-kraken2-gives-very-different-results/698 "2020-07-09T20:36:31Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![MaryamTarazkar](https://avatars.discourse-cdn.com/v4/letter/m/4da419/32.png) [@MaryamTarazkar](https://forum.biobakery.org/u/MaryamTarazkar)\
**Post date:** [July 9, 2020, 8:36pm UTC](https://forum.biobakery.org/t/metaphlan2-and-kraken2-gives-very-different-results/698/1 "2020-07-09T20:36:31Z")

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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

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**Author:** ![ddavey](https://avatars.discourse-cdn.com/v4/letter/d/53a042/32.png) [@ddavey](https://forum.biobakery.org/u/ddavey)\
**Post date:** [September 13, 2020, 8:35am UTC](https://forum.biobakery.org/t/metaphlan2-and-kraken2-gives-very-different-results/698/2 "2020-09-13T08:35:42Z")

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me too. This problem confounded me a lot.

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**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [September 14, 2020, 9:05am UTC](https://forum.biobakery.org/t/metaphlan2-and-kraken2-gives-very-different-results/698/3 "2020-09-14T09:05:01Z")

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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](https://github.com/biobakery/MetaPhlAn/issues/90)