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Is it common that only about 30 MAGs of high quality were obtained from one metagenome sample? #37

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Dear Hongzhong,

That sounds good actually, I generally got similar results from my human gut microbiome samples.
If I recall correctly, the largest gut community of GEMs we simulated in the metaGEM paper had around 60 members (all reconstructed from a single sample), but most samples had ~30 GEMs.
Of course the results will vary depending on the microbiome environment, sample complexity, sequencing depth, etc.

However, bear in mind that you can also use the medium quality MAGs to generate GEMs for simulation. In the paper (Fig. 2b) we showed that although GEMs from HQ MAGs tend to have more genes than GEMs from MQ MAGs, they show a very similar distribution in the number of reactions and …

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@franciscozorrilla
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Converted from issue

This discussion was converted from issue #24 on May 10, 2021 11:32.