# Dereplicate

This workflow automates the dereplication of your collection of genomes, Metagenome-Assembled Genomes (MAGs), or Single-Cell Amplified Genomes (SAGs).

To execute the workflow, run:

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

For additional options, run:

```bash
miga derep_wf -h
```

Importantly, the dereplication can be performed on ANI (default) or AAI (passing the `--aai` flag) at a given threshold (by default 95%) that can be modified with the flag `--threshold`. Finally, the representative genomes can be selected to reflect the highest genome quality (default) or to be the most "central" genome in the clade in ANI or AAI space (passing the `--medoids` flag).

## Expected output

Once your run is complete, you may expect the [standard summaries](https://manual.microbial-genomes.org/part6/summaries) for `cds`, `assembly`, and `essential_genes`, as well as a table (`genomospecies.tsv`) with three columns: (1) a clade name, (2) the name of the representative genome, and (3) the names of all the members in the clade separated by commas. Additionally you can expect the subdirectory `representatives` including assemblies (FastA files, nucleotides) of all representative genomes. This is the dereplicated set of genomes.