What's the difference of Metaphlan2 output on strain level and StrainPhlan

yun li

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Oct 12, 2016, 12:20:23 PM10/12/16

to MetaPhlAn-users

Hi,
I have some question on the Metaphlan2 output and StrainPhlan. I am trying to use strainPhlan. However, when I checked my metaphlan2 default output, there also have strain level results. So my question is what is the difference between metaphlan2 strain level output and StrainPhlan. I would also like to know where I can get any description on strainphlan algorithm(which paper I should read?).

Thanks,
Yun

Duy Tin Truong

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Oct 13, 2016, 4:31:33 AM10/13/16

to yun li, MetaPhlAn-users

Hi Yun,

MetaPhlAn2 strain level output is the presence/absence of the species-specific markers whereas the StrainPhlAn strain level result is the nucleotide strains of the subject/species from the metagenomic samples and those strains are built from the MetaPhlAn2 markers. From StrainPhlAn strains, you can also build the phylogentic trees.

Cheers,

Tin

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yun li

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Oct 14, 2016, 10:55:00 AM10/14/16

to Duy Tin Truong, MetaPhlAn-users

I still can not understand. why I can see strain level using the species-specific markers in MetaPhlan2?

what is the meaning of "nucleotide strains of the subject/species from the metagenomic samples" ?

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Nicola Segata

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Oct 14, 2016, 12:03:20 PM10/14/16

to yun li, Duy Tin Truong, MetaPhlAn-users

Hi Yun,

strain-level analysis inside MetaPhlAn2 is kind of a preliminary version of what we then called PanPhlAn (http://www.nature.com/nmeth/journal/v13/n5/full/nmeth.3802.html).

StrainPhlAn takes instead a slightly different route as strains are characterized based on differences at the sequence level (single-nucleotide-variants) of species specific markers. StrainPhlAn uses the "sam" output of MetaPhlAn2.

PanPhlAn and StrainPhlAn are complementary tools (the first looks at the gene content of strains, the second at their "genetics") are we recommend them over the strain-level analysis inside MetaPhlAn2 that is kept for retro-compatibility.

I hope this helps

thanks

Nicola

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