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wwood / singlem

Novelty-inclusive microbial community profiling of shotgun metagenomes
http://wwood.github.io/singlem/
GNU General Public License v3.0
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Do singleM result be suitable for phylogenetic tree? #137

Open LiZhihua1982 opened 12 months ago

LiZhihua1982 commented 12 months ago

Hi Thank you very much for your singleM. I want to know whether singleM result suitable for constructing phylogenetic tree as it produce a relative short sequences? if possible, which gene is better? Thanks

wwood commented 11 months ago

Hi,

I think that just the 60bp or 20aa translations don't hold a lot of signal individually, but can do in aggregate. So the answer to your question depends on what you hope to interpret from the analysis.

Is the idea to compute phylogenetics based metrics like unifrac?

LiZhihua1982 commented 11 months ago

Dear Dr.Ben J Woodcroft, Thank you very much for your reply! The reason that I ask this question is to want to bridge the meatgenomics data to quantitatively infer community assembly mechanisms using the attached file(Ning et al., 2020, Nature Communications), which it is 16SrRNA and ITS OTU/ASV as inputs(http://ieg3.rccc.ou.edu:8080). Would you please see the attached file and give me some advices? Thanks again!

Best regards

Li Zhihua

发件人: Ben J Woodcroft @.> 发送时间: 2023年9月3日 11:43 收件人: wwood/singlem @.> 抄送: Li Zhihua @.>; Author @.> 主题: Re: [wwood/singlem] Do singleM result be suitable for phylogenetic tree? (Issue #137)

Hi,

I think that just the 60bp or 20aa translations don't hold a lot of signal individually, but can do in aggregate. So the answer to your question depends on what you hope to interpret from the analysis.

Is the idea to compute phylogenetics based metrics like unifrac?

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wwood commented 11 months ago

Hi again,

Ah, OK. I'm not sure about that. You could try treating each of the OTUs separately for each OTU table (probably concentrating just on the genes which target both bacteria and archaea - see singlem metapackage --describe), but I don't have a good feeling for how that would work with inferring assembly mechanisms, and in particular how that would compare to doing the same thing with 16S/ITS.

If you wanted to test it one thing you could try is to see what the answers that each provides when applied to some EMP500 samples maybe, where both analyses have been done? https://earthmicrobiome.org/emp500/