PICRUST2 Reference database

[Sara Beier]

Hi Gavin,

I am wondering, does the new reference database for PICRUSt2 also contain genome data from metagenome assembled genomes (MAGs)?

Best,

Sara

[Gavin Douglas]

Hi there,

No it does not - they are only reference genomes from IMG.

Cheers,

Gavin

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[Sara Beier]

Hi Gavin,

thanks for you fast response. I have asked the question, because definitely there are some single amplified genomes (SAGs) in the IMG database that are also in the PICRUSt2 reference database, e.g. 2681812878 (Alphaproteobacteria bacterium SAG AG-538-F13, from the project 'Dark ocean microbial single cell genomics'). I also found some IMG entries from projects including metagenomes, e.g. 2561511235 (Blastococcus sp. URHD0036 from the project 'Mediterranean Grassland Soil Metagenome (MGSM): Enabling a systems view of soil carbon and nitrogen biogeochemistry under a changing climate.'). In this case I was wondering if this could be a MAG? Anyway, maybe I should pose this question to IMG.

Cheers,

Sara

[Gavin Douglas]

Hi Sara,

Ah I see - that does sound like a question for IMG.

Cheers,

Gavin

On May 27, 2021, at 7:57 AM, Sara Beier <sara....@io-warnemuende.de> wrote:

Hi Gavin,

thanks for you fast response. I have asked the question, because definitely there are some single amplified genomes (SAGs) in the IMG database that are also in the PICRUSt2 reference database, e.g. 2681812878 (Alphaproteobacteria bacterium SAG AG-538-F13, from the project 'Dark ocean microbial single cell genomics'). I also found some IMG entries from projects including metagenomes, e.g. 2561511235 (Blastococcus sp. URHD0036 from the project 'Mediterranean Grassland Soil Metagenome (MGSM): Enabling a systems view of soil carbon and nitrogen biogeochemistry under a changing climate.'). In this case I was wondering if this could be a MAG? Anyway, maybe I should pose this question to IMG.

Cheers,

Sara

On Thursday, 27 May 2021 at 13:35:09 UTC+2 Gavin Douglas wrote:

Hi there,

No it does not - they are only reference genomes from IMG.

Cheers,

Gavin

On May 27, 2021, at 7:07 AM, Sara Beier <sara....@io-warnemuende.de> wrote:

Hi Gavin,

I am wondering, does the new reference database for PICRUSt2 also contain genome data from metagenome assembled genomes (MAGs)?

Best,

Sara

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