> For the complete documentation index, see [llms.txt](https://manual.microbial-genomes.org/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://manual.microbial-genomes.org/master/part6/quality_wf.md).

# Quality

This workflow automates the evaluation of quality statistics on your genomes, Metagenome-Assembled Genomes (MAGs), or Single-Cell Amplified Genomes (SAGs).

To execute the workflow, run:

```bash
miga quality_wf -o my_project path/to/mags/*.fasta
```

For additional options, run:

```bash
miga quality_wf -h
```

## Expected output

Once your run is complete, you may expect the [standard summaries](/master/part6/summaries.md) for `cds`, `assembly`, `essential_genes`, and `ssu`. In addition, if you pass the option `--mytaxa-scan`, you can expect the subdirectory `mytaxa_scan` including PDF reports for each input genome.


---

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