diff --git a/README.md b/README.md index 9d23a34..c80b5da 100644 --- a/README.md +++ b/README.md @@ -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 -a -d +``` + +*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