A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes. It includes ten models added to the metagenome mode:
- Acanthamoeba polyphaga mimivirus
- Paramecium bursaria Chlorella virus
- Acanthocystis turfacea Chlorella virus
- VirSorter2's NCLDV gene model
- Topaz (genetic code 15)
- Agate (genetic code 15)
- Gut phages (genetic code 15)
- Gut phages (genetic code 11) × 5
If you use prodigal-gv, please cite:
Camargo, A. P., Roux, S., Schulz, F., Babinski, M., Xu, Y., Hu, B., ... and Kyrpides, N. C. (2023). Identification of mobile genetic elements with geNomad. Nature Biotechnology, 1-10.
Prodigal was written by Doug Hyatt and its usage should be acknowledged.
Hyatt, D., Chen, G.-L., LoCascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. (2010). Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119.
prodigal-gv can be installed via Conda/Mamba, pre-build binaries (Linux and macOS), or built from scratch:
# Conda/Mamba:
conda install -c bioconda prodigal-gv
# Pre-built binary (Linux):
curl -L https://github.com/apcamargo/prodigal-gv/releases/download/2.10.0/prodigal-gv-linux -o prodigal-gv
chmod +x prodigal-gv
# Pre-built binary (macOS):
curl -L https://github.com/apcamargo/prodigal-gv/releases/download/2.10.0/prodigal-gv-macos -o prodigal-gv
chmod +x prodigal-gv
# Buld from scratch
git clone https://github.com/apcamargo/prodigal-gv.git
cd prodigal-gv
make
prodigal-gv -p meta -i genome.fna -a proteins.faa > /dev/null 2>&1parallel-prodigal-gv.py is a script that allows parallelized execution of prodigal-gv:
./parallel-prodigal-gv.py -t 8 -q -i genome.fna -a proteins.faa