Binning tools for metagenomics
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2.1 years ago
loisveillat ▴ 10

Hi,

I'm doing a metagenomic analysis on anvio and want to do automatic binning. However, I have a single sample and most of the tools mentioned in the anvio tutorial are hybrid binning tools, adapted to several samples ( GROOPM, MAXBIN, METABAT, BINSANITY_REFINE, MYCC and CONCOCT).

Do you know of tools adapted to single samples?

Thank you for your help

Loïs

binning anvio metagenomics sample concot • 1.7k views
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Metabat can work with a single sample. It will only use the tetra-nucleotide distribution information though.

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2.1 years ago
onestop_data ▴ 300

Please check this out. Here I describe in details how to use CONCOT and Metabat

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It is nice to have this tutorial as a guideline. Still, some of its conclusions are fairly simplistic. For example, even though in your hands CONCOCT has identified 16 bins from 10 species, that didn't overestimate the number of species because 9 of those 16 bins have 0% completeness and 12 have <10% completeness.

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great point, but it is important to remember that it is a metagenomic dataset, so there is not enough coverage to recover the full genome, thus the complement is low for many of the bins.

I have added some extra words to the conclusion to make it more clear. thanks

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