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Mention pyrodigal-gv CLI in README.md [ci skip]
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althonos committed Nov 27, 2023
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Expand Up @@ -74,6 +74,17 @@ for i, pred in enumerate(orf_finder.find_genes(bytes(record.seq))):
`ViralGeneFinder` has an additional keyword argument, `viral_only`, which can
be set to `True` to run gene calling using only viral models.

## 🔨 Command line

`pyrodigal-gv` comes with a very simple command line similar to Prodigal and `pyrodigal`:
```console
$ pyrodigal-gv -i <input_file.fasta> -a <gene_translations.fasta> -d <gene_sequences.fasta>
```

*Contrary to `prodigal` and `pyrodigal`, the `pyrodigal-gv` script runs in **meta** mode
by default! Running in **single** mode can be done with `pyrodigal-gv -p single` but
the results will be exactly the same as `pyrodigal`, so why would you ever do this ⁉️*


## 🔖 Citation

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