# Should I use kneaddata in the following condition?

**URL:** <https://forum.biobakery.org/t/should-i-use-kneaddata-in-the-following-condition/890>\
**Category:** KneadData\
**Created:** [August 21, 2020, 9:46pm UTC](https://forum.biobakery.org/t/should-i-use-kneaddata-in-the-following-condition/890 "2020-08-21T21:46:50Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![DEEPCHANDA7](https://avatars.discourse-cdn.com/v4/letter/d/eb9ed0/32.png) [@DEEPCHANDA7](https://forum.biobakery.org/u/DEEPCHANDA7)\
**Post date:** [August 21, 2020, 9:46pm UTC](https://forum.biobakery.org/t/should-i-use-kneaddata-in-the-following-condition/890/1 "2020-08-21T21:46:50Z")

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Hi @franzosa @fbeghini !!!  
I have profiled shotgun data with MetaPhlAn 3.0 with `--ignore_eukaryotes --ignore_archaea`. The output abundance now will be used as input of HUMAnN 3.0. In this context, should I use Kneaddata before the MEtaPhlAn step? Can’t I directly use the metagenome sequences as input for HUMAnN and MetaPhlAn without the Kneaddata step? Will not HUMAnN be able to discard the host reads?

Thanks,  
DC7

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**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [August 28, 2020, 1:27pm UTC](https://forum.biobakery.org/t/should-i-use-kneaddata-in-the-following-condition/890/2 "2020-08-28T13:27:57Z")

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Hi @DEEPCHANDA7,

It is recommended to run Kneaddata quality control step before moving on to downstream analysis and profiling(MetaPhlAn 3.0 and HUMAnN 3.0). It is easier to remove the host contaminant reads using Kneaddata ([see more details here on how to use bowtie2 using Kneaddata](https://github.com/biobakery/biobakery/wiki/kneaddata#contaminant-databases)).

Also, additional information on kneaddata available here, [http://huttenhower.sph.harvard.edu/kneadData](http://huttenhower.sph.harvard.edu/kneadData).

Thanks,  
Sagun