# Kneaddata output as input for metaphlan

**URL:** <https://forum.biobakery.org/t/kneaddata-output-as-input-for-metaphlan/8519>\
**Category:** KneadData\
**Created:** [September 24, 2025, 12:53pm UTC](https://forum.biobakery.org/t/kneaddata-output-as-input-for-metaphlan/8519 "2025-09-24T12:53:36Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Jose\_Freixas](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jose_freixas/32/3342_2.png) [@Jose\_Freixas](https://forum.biobakery.org/u/Jose_Freixas)\
**Post date:** [September 24, 2025, 12:53pm UTC](https://forum.biobakery.org/t/kneaddata-output-as-input-for-metaphlan/8519/1 "2025-09-24T12:53:36Z")

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Hello, I appreciate anyone’s input on this. As the kneaddata output yields 4 major files (paired and unmatched) that I would like to use for downstream analysis (i.e., metaphlan), can I catenate them into one fastq file? I understand paired end reads come from the same DNA fragment, how would this approach (cat) avoid biases in counts or abundances?

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**Author:** ![tkuntz-hsph](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/tkuntz-hsph/32/492_2.png) [@tkuntz-hsph](https://forum.biobakery.org/u/tkuntz-hsph)\
**Post date:** [September 30, 2025, 2:42pm UTC](https://forum.biobakery.org/t/kneaddata-output-as-input-for-metaphlan/8519/2 "2025-09-30T14:42:47Z")

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Hi,  
Yes, you should cat your kneaddata output files into one fastq file for metaphlan. This is the standard procedure used in the biobakery workflows [GitHub - biobakery/biobakery\_workflows: bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.](https://github.com/biobakery/biobakery_workflows/tree/master). Biases in counts and abundances are accounted for by how metaphlan calculates relative abundance, including information such as coverage and species genome length.