Option to use Prodigal-gv
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snayfach commented
Prodigal-gv is a fork of Prodigal v2.6.3 that was modified to improve detection of alternative genetic codes (especially 4 and 15), which are not uncommon in certain phages families. Standard Prodigal (with or without -p meta) doesn't do a good job of detecting these cases, resulting in highly fragmented gene predictions. Given that CRISPR systems have been found in phages, it would be nice if this gene caller was an option when using cc-typer. The command line options are identical to standard prodigal, except the name of the program is prodigal-gv instead of prodigal.
https://github.com/apcamargo/prodigal-gv
https://anaconda.org/bioconda/prodigal-gv