# Classify

This workflow automates the comparison of your genomes, Metagenome-Assembled Genomes (MAGs), or Single-Cell Amplified Genomes (SAGs) against a reference project for taxonomy.

A reference project has to be a separate MiGA project with a database of your choice, taxonomically annotated, and fully indexed. If you want to use the pre-processed database provided by MiGA Online, run:

```bash
miga download
```

To execute the workflow, run:

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

For additional options, run:

```bash
miga classify_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 `taxonomy`, as well as a summary classification table (`classification.tsv`) with two columns: (1) the genome name, and (2) the space-delimited classification of the genome with taxon names prefixed by the rank code and a colon. Something like:

```
NZ_CP010409_1    d:Bacteria p:Proteobacteria c:Gammaproteobacteria o:Xanthomonadales f:Xanthomonadaceae g:Xanthomonas s:Xanthomonas_sacchari
NZ_CP016878_1    d:Bacteria p:Proteobacteria c:Gammaproteobacteria o:Xanthomonadales f:Xanthomonadaceae g:Xanthomonas s:Xanthomonas_hortoru
[...]
```


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# Agent Instructions: Querying This Documentation

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

```
GET https://manual.microbial-genomes.org/master/part6/classify_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.