# StrainPhlAn for detection of known strains in mixed-strain samples

**URL:** https://forum.biobakery.org/t/strainphlan-for-detection-of-known-strains-in-mixed-strain-samples/8850
**Category:** StrainPhlAn
**Created:** [March 31, 2026, 5:26pm UTC](https://forum.biobakery.org/t/strainphlan-for-detection-of-known-strains-in-mixed-strain-samples/8850 "2026-03-31T17:26:55Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![ttmgr](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ttmgr/32/3612_2.png) [@ttmgr](https://forum.biobakery.org/u/ttmgr)
#### Post date: [March 31, 2026, 5:26pm UTC](https://forum.biobakery.org/t/strainphlan-for-detection-of-known-strains-in-mixed-strain-samples/8850/1 "2026-03-31T17:26:55Z")

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Hi,

I have nanopore metagenomic samples and I am looking to detect the presence of 4 known L. monocytogenes strains (reference genomes available).

I have seen it suggested to:

- Use a single reference genome for mapping
- Then rely on StrainPhlAn’s marker gene knowledge to differentiate between the strains

My understanding however is that StrainPhlAn reconstructs a single consensus sequence per species per sample from marker genes, meaning:

1. If a sample contains multiple strains simultaneously, the output would be a chimeric consensus rather than detection of individual strains — is this correct?

2. Is StrainPhlAn designed for reference-based detection of specific known strains, or primarily for phylogenetic comparison of the  
dominant strain across samples?

Thanks!