Annotate outsource bins

[JK Hong]

Hi,

I was notified that bins having high or medium quality was not found through the IMG/M pipeline. So, I conducted a binning process on my own through DAS tool using bins created from the maxbin and metabat program. By doing so, I found medium quality bins.

Now, I want to annotate the contigs in the medium quality bins with annotation results from the IMG/M pipeline. But I don't know how. I couldn't find any application in IMG/M, so if anyone has any experience and tips for this situation, I would like to ask them to share their knowledge.

Thank you.

Jin-Kyung Hong

[Scott Thomas]

One way might be to work backward from your current bins and link the ORFs in your bins to the ones in the metagenome on IMG, which is probably annotated.

Cheers,

Scott 

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[Emiley Eloe-Fadrosh]

It is often the case that other binning algorithms will identify different bins, and using multiple tools can improve the results, along with different parameters used with the same tool. The automated IMG binning pipeline using a single tool, MetaBAT, and using the MIMAG standards (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436528) to designate quality based on checkM completeness and contamination metrics, along with presence of rRNA and tRNA genes. Further information can be found here: https://img.jgi.doe.gov/cgi-bin/mer/main.cgi?section=MetagenomeBins&page=info or in the IMG/M publication.

If you used the assembled and annotated metagenome from IMG in your binning processing, you should be able to identify the corresponding contigs from your bin of interest and use that to generate scaffold sets in IMG if you wish to further analyze your data in IMG. Further details can be found here for how to perform this function for scaffold carts: https://img.jgi.doe.gov/docs/IMGWorkspaceUserGuide.pdf