<p>Some papers check 5S, 16S, 23S and ≥18 tRNA genes for completeness. For example, you can see <a href="https://www.nature.com/articles/s41467-021-22203-2" rel="nofollow noreferrer">this paper</a>.</p>

CC BY-SA 4.0
2021-12-04T15:27:53.583Z
2021-12-04T15:27:53.583Z
user172818
<p>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.</p>

CC BY-SA 4.0
2021-12-05T00:14:21.850Z
2021-12-05T00:14:21.850Z
Avamys
<p>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 &gt; Megahit for assembly &gt; vamb for binning). What else could I do / where do I go from here? (especially regarding quality control)</p>

<assembly><metagenome><quality-control>
What are some ways to check metagenomic bin quality?
# What are some ways to check metagenomic bin quality?

(Asked by: username_0 on 2021-12-03)

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)

**Tags:** assembly, metagenome, quality-control

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## 2 answers

### Answer by username_1 on 2021-12-04. Score: 1 | Accepted answer

Some papers check 5S, 16S, 23S and ≥18 tRNA genes for completeness. For example, you can see [this paper](https://www.nature.com/articles/s41467-021-22203-2).


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### Answer by username_2 on 2021-12-05. Score: 1

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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