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I am new to metagenomic binning. I've used CheckM in order to estimate completeness and contamination values, and most of my bins of interest appear to have good values. My workflow was pretty straightforward (BBDuk for quality control > Megahit for assembly > vamb for binning). What else could I do / where do I go from here? (especially regarding quality control)

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Some papers check 5S, 16S, 23S and ≥18 tRNA genes for completeness. For example, you can see this paper.

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There are many other tools. If you want to get nice statistics and graphs I recommend Amber, there is also Anvio for manual refinement of the bins.

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