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What is the difference between "phylophlan" database and "SGB.XXX"? #116

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augfranco93 opened this issue Oct 3, 2023 · 2 comments
Open

What is the difference between "phylophlan" database and "SGB.XXX"? #116

augfranco93 opened this issue Oct 3, 2023 · 2 comments

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@augfranco93
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Hi,
Hope you are well.
I'm working in a metagenomic analysis, and I want to use phylophlan_metagenomic module. Exist any difference between "phylophlan" database and "SGB.XXX"? Which is better to run the module that I want?

Thank you very much.
@MapleHe
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MapleHe commented Mar 21, 2024 •
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As I understand, phylophlan database is for phylogeny analysis analysis, used in main function of PhloPhlAn.

SGB.XXX are specific database for taxon (SGB) assignment, used in phylophlan_metagenomic module. So I think SGB.xxx is what you may want. And it seems that the module should download the database files automatically.

Update:
It seems that in the latest version of phylophlan, the module has been renamed to phylophlan_assign_sgbs

@ScienceAdvances
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phylophlan_metagenomic renamed to phylophlan_assign_sgbs!!! Thanks for notifying

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@MapleHe @ScienceAdvances @augfranco93