Getting strain counts from StrainPhlAn

Dear Authors,

I have a non-gut shotgun data (fastq files) and I want to get the abundance tables for the strain types. Is that something I can do using StrainPhlAn?

I followed the manual and I’ve got to the point where I have the pickle files for each sample, containing the markers+sequences. But I’m not sure how I can get the count/abundance for the strains.

Thanks in advance for your help,


unfortunately you cannot do such thing with StrainPhlAn.
By using MetaPhlAn, you will get an abundance table for the species and then using StrainPhlAn you can get a phylogenetic tree of strains of a specific species. However you cannot get the relative abundance of individual strains from the same sample.


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Hi Leonard,

Thanks so much for the quick and complete response. Do you by any chance know if there is a tool out there that I can use to get the relative abundance of individual strains?


You could do it “manually” using MetaPhlAn + StrainPhlan, reference genomes, maybe isolates and intermediates results of mapping…but that would be rather tedious and would need you to design the whole analysis.

Maybe try strainFLAIR (StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs [PeerJ]), it seems to be doing what you want to do

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Got you. Thanks so much!