# Run StrainPhlAn with output from nf-core/taxprofiler x MetaPhlAn?

**URL:** https://community.seqera.io/t/run-strainphlan-with-output-from-nf-core-taxprofiler-x-metaphlan/2330
**Category:** Ask for help
**Tags:** nf-core
**Created:** [August 12, 2025, 11:05am UTC](https://community.seqera.io/t/run-strainphlan-with-output-from-nf-core-taxprofiler-x-metaphlan/2330 "2025-08-12T11:05:43Z")
**Posts on this page:** 1
**Page:** 1

<div class="post-metadata">

### Author: ![mr2raccoon](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mr2raccoon/32/1949_2.png) [@mr2raccoon](https://community.seqera.io/u/mr2raccoon)
#### Post date: [August 12, 2025, 11:05am UTC](https://community.seqera.io/t/run-strainphlan-with-output-from-nf-core-taxprofiler-x-metaphlan/2330/1 "2025-08-12T11:05:44Z")

</div>

Hey,

I am an absolute beginner in metagenomics and maybe you can help.

After successfully completing metagenomic analysis of my samples and subsequent analysis of differential abundance of certain taxa, I would like to analyze to which bacterial strain the belong to.

Is it possible to chain StrainPhlAn to the output generated with nf-core/taxprofiler? After reading the [StrainPhlan-documentation](https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-4.1), I leanred that I need the `SAM files (*.sam.bz2)` generated by MetaPhlan for running StrainPhlan. However, when searching my `results/ `output-directory, I could not detect them. Is there -flagable options when running taxprofiler to have the `SAM files (*.sam.bz2) `saved?

Thank you for any advice!

Best,