> 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/part6/preproc_wf.md).

# Preprocess

This workflow automates the preprocessing of your genomic or metagenomic datasets.

To execute the workflow, run:

```bash
miga preproc_wf -o my_project -i raw_reads_single path/to/reads/*.fastq
```

Supported inputs include:

* *raw\_reads\_single:* Single raw reads in a single FastQ file
* *raw\_reads\_paired:* Paired raw reads in two FastQ files
* *trimmed\_reads\_single:* Single trimmed reads in a single FastA file
* *trimmed\_reads\_paired:* Paired trimmed reads in two FastA files
* *trimmed\_reads\_interleaved:* Paired trimmed reads in a single FastA file
* *assembly:* Assembled contigs or scaffolds in FastA format

For additional options, run:

```bash
miga preproc_wf -h
```

## Expected output

Once your run is complete, you may expect the [standard summaries](/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.