Question

Difference between a bin and a MAG

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2.7 years ago

Maria Laura ▴ 30

Hello,

I am aware that binning is an important step for reconstructing metagenome-assembled genomes (MAGs).

Once I complete the binning, I have a folder with several bins. Can I directly consider them MAGs?

Is there any standard criteria to classify a bin as a MAG? Or an extra step after binning that I am not aware of?

metagenomics mags binning • 3.6k views

ADD COMMENT • link updated 2.3 years ago by v.berriosfarias ▴ 140 • written 2.7 years ago by Maria Laura ▴ 30

score 6 · Answer 1 · 2021-07-23

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2.7 years ago

Mensur Dlakic ★ 27k

What Nitin Narwade said.

Basically, MAGs are bins that have been checked for completeness and refined if necessary. Any of your bins that are >90% complete and <10% contaminated can be considered MAGs as they are. Some people will even say >70% complete and <10% contaminated already qualifies as a MAG.

Yet if your bin is only 30% complete, or maybe 100% complete but 300% contaminated, you will have to work on them before they can be considered MAGs.

ADD COMMENT • link 2.7 years ago by Mensur Dlakic ★ 27k

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Thank you very for the help!!!

ADD REPLY • link 2.7 years ago by Maria Laura ▴ 30

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Hello Mensur, do you have any cite of this so I can add it to my thesis references?

Thanks for this answer

ADD REPLY • link 2.3 years ago by v.berriosfarias ▴ 140

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The following paper explains some of the topics we discussed:

https://pubmed.ncbi.nlm.nih.gov/28787424/

ADD REPLY • link 2.3 years ago by Mensur Dlakic ★ 27k

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thanks so much.

ADD REPLY • link 2.3 years ago by v.berriosfarias ▴ 140

score 4 · Answer 2 · 2021-07-23

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2.7 years ago

Nitin Narwade ★ 1.6k

Well, it is always advisable to check the bin quality before declaring it as MAG.

Usually, after binning, I try and assess its quality using checkM, along with some additional parameters such as the number of predicted genes per bin, assembly size, coverage, GC content, and etc. Also, I predict the organism-specific phylogenetic markers such as 16S rRNA or ITS and then search them in the database to check whether the predicted bins have any contamination OR not.