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motu-tool / mOTUs

motus - a tool for marker gene-based OTU (mOTU) profiling
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Availability of MAGs representative of meta-mOTUs #63

Closed fplazaonate closed 2 years ago

fplazaonate commented 3 years ago

Hi,

Representative genomes of ref-mOTUs are available on proGenomes. I was wondering if MAGs representative of meta-mOTUs are available as well?

Best, Florian

AlessioMilanese commented 3 years ago

Dear Florian,

We added now a pre-print with all the marine MAGs and genomes: https://www.biorxiv.org/content/10.1101/2021.03.24.436479v1

And the human associated MAGs can be found in: https://pubmed.ncbi.nlm.nih.gov/30661755/ https://www.nature.com/articles/s41587-020-0603-3 https://www.nature.com/articles/s41586-019-1058-x

Best, alessio

Lucas-Maciel commented 2 years ago

Dear @AlessioMilanese

I have done some biomarkers discovery based on the mOTUS and now I have a list of 100 mOTUS from ref, meta and extension databases. I want to download the genomes of these species and make annotations to identify the presence of some pathways.

Do you think that there is any way to provide a unique database with all genomes that you have used to identify the MGs and their mOTUs IDs? Just to make it easier to go deeper in the analysis instead of having to manually search in each one of these links.

Kind regards

AlessioMilanese commented 2 years ago

Dear @Lucas-Maciel

For ref-mOTUs there are genome sequences available in progenomes 2 (https://progenomes.embl.de/). The ref-mOTU identifier map to the specI identifier (the specI id specI_v3_Cluster10 correspond to the ref-mOTU 10).

Regarding meta- and ext-mOTUs is a little bit more complicated. Are you working in human gut?

Lucas-Maciel commented 2 years ago

@AlessioMilanese thanks for your fast reply.

Yes I work with human gut.

I was looking the progenomes but I was only able to manually download one by one using the specI clusters in the website. I also download the representatives contigs fasta files but they were all in one single file and no cluster information. Maybe I'm not looking in the right place.

AlessioMilanese commented 2 years ago

Since you are working with human gut you might be interested in: https://www.nature.com/articles/s41587-020-0603-3

that we use also for mOTUs 3.

I was looking the progenomes but I was only able to manually download one by one using the specI clusters in the website. I also download the representatives contigs fasta files but they were all in one single file and no cluster information. Maybe I'm not looking in the right place.

I'm not sure about this. Can you contact the first author?