prodigal-gv

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

Citation

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.

Installation

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

Usage

prodigal-gv -p meta -i genome.fna -a proteins.faa > /dev/null 2>&1

Parallelized execution

parallel-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