# 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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# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://manual.microbial-genomes.org/master/part6/quality_wf.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.