Getting strain counts from StrainPhlAn

Microbial community profiling StrainPhlAn
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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?

P.S.
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,
Mo

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Hello,

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.

Léonard

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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?

Thanks,
Mo

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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!

Mo