A simple script to run prodigal on a genome FASTA file, using code/thresholds from GTDB-tk to decide on various parameters for prodigal. Prodigal is run twice, once using translation table 4 and once with 11, and the gene predictions for one of these options is chosen.
The only dependency is the SingleM package, since further dependencies such as prodigal are included underneath. To use:
mamba create -n singlem -c conda-forge -c bioconda singlem
mamba activate singlem
./bin/prodigal-runner run -h
./bin/prodigal-runner run -i /path/to/genome.fasta -o /path/to/output_directory -t NUM_THREADS
Citation
Since this is just a wrapper around GTDB-tk, please cite the GTDB-tk paper if you use this script:
Chaumeil, Pierre-Alain, Aaron J. Mussig, Philip Hugenholtz, and Donovan H. Parks. "GTDB-Tk v2: memory friendly classification with the genome taxonomy database." Bioinformatics 38, no. 23 (2022): 5315-5316.