# Index

This workflow automates the indexing of your genomic collection.

To execute the workflow, run:

```bash
miga index_wf -o my_project path/to/genomes/*.fasta
```

For additional options, run:

```bash
miga index_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`. Additionally all the intermediate files are preserved, including assemblies, predicted genes, and detected essential and ribosomal genes. Importantly, all-vs-all comparisons are generated using Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), making this a queriable project.

## Indexing publicly available genomes

It is also possible to use this workflow on genomes publicly available in NCBI. This enables taxonomic analysis, such as using this indexed project as a reference database for the [classification workflow](/master/part6/classify_wf.md).

For example, to download and index all the genomes from the species **Xanthomonas vesicatoria** using Diamond for AAI and FastANI for ANI estimation (`--fast` flag), run:

```bash
miga index_wf -o X_vesicatoria \
  -T 'Xanthomonas vesicatoria' --project-type clade --fast -v
```


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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/index_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.