# StrainPhlAn Usage for Bacterial SNP Annotation

**URL:** <https://forum.biobakery.org/t/strainphlan-usage-for-bacterial-snp-annotation/6461>\
**Category:** StrainPhlAn\
**Created:** [January 14, 2024, 6:20pm UTC](https://forum.biobakery.org/t/strainphlan-usage-for-bacterial-snp-annotation/6461 "2024-01-14T18:20:00Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Phoenix\_xu](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/phoenix_xu/32/2648_2.png) [@Phoenix\_xu](https://forum.biobakery.org/u/Phoenix_xu)\
**Post date:** [January 14, 2024, 6:20pm UTC](https://forum.biobakery.org/t/strainphlan-usage-for-bacterial-snp-annotation/6461/1 "2024-01-14T18:20:00Z")

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Hello everyone,

I have some questions regarding the analysis outputs. Concerning the .fna files located in the output/tmp/clean\_dna directory, do these files encompass all the reads mapped to the markers and classified to the species? I am specifically looking for files that contain the reads mapped to the reference genome of the species and exclude reads assigned with the same likelihood to more than one species. Additionally, I am interested in using StrainPhlAn to annotate bacterial SNPs.

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**Author:** ![Michal\_Puncochar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/michal_puncochar/32/2321_2.png) [@Michal\_Puncochar](https://forum.biobakery.org/u/Michal_Puncochar)\
**Post date:** [March 18, 2024, 1:12pm UTC](https://forum.biobakery.org/t/strainphlan-usage-for-bacterial-snp-annotation/6461/2 "2024-03-18T13:12:45Z")

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Hello

to get reads that map against markers – you have to look at the .sam output of metaphlan, it’s exactly that: alignment of reads to the Metaphlan markers. By design of the database no reads should be alignable to more than one marker.

As for the bacterial SNPs, Strainphlan produces a consensus strain masking out polymorphic positions with \*, so you can look for those in the output of sample2markers. For anything more sophisticated I suggest running samtools pileup manually on the sam file or use some dedicated SNP analysis tools.

Best  
Michal

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**Author:** ![Ali\_Rahnavard](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ali_rahnavard/32/653_2.png) [@Ali\_Rahnavard](https://forum.biobakery.org/u/Ali_Rahnavard)\
**Post date:** [May 23, 2024, 3:07pm UTC](https://forum.biobakery.org/t/strainphlan-usage-for-bacterial-snp-annotation/6461/3 "2024-05-23T15:07:01Z")

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Hi Michal,

StrainPhaln outputs include a MSA file of aligned marker genes for samples in the study. We have developed a tool, deepBreaks ([GitHub - omicsEye/deepbreaks](https://github.com/omicsEye/deepBreaks)) that prioritize and rank SNVs using the MSA file that are associated with a metadata of interest (e.g., health-disease and niche of samples). deepBreaks provide multiple applications and one is analyzing starinphlan outputs for HMP project ([deepbreaks/examples/discrete\_phenotype\_HMP.ipynb at master · omicsEye/deepbreaks · GitHub](https://github.com/omicsEye/deepbreaks/blob/master/examples/discrete_phenotype_HMP.ipynb))

Please let us know if you need help running deepBreaks.

Ali