prokka
Prokka is a pipeline for rapidly annotating prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.
Detailed usage can be found here: https://github.com/tseemann/prokka
Link to section 'Versions' of 'prokka' Versions
- 1.14.6
Link to section 'Commands' of 'prokka' Commands
- prokka
- prokka-abricate_to_fasta_db
- prokka-biocyc_to_fasta_db
- prokka-build_kingdom_dbs
- prokka-cdd_to_hmm
- prokka-clusters_to_hmm
- prokka-genbank_to_fasta_db
- prokka-genpept_to_fasta_db
- prokka-hamap_to_hmm
- prokka-tigrfams_to_hmm
- prokka-uniprot_to_fasta_db
Link to section 'Module' of 'prokka' Module
You can load the modules by:
module load biocontainers
module load prokka
Link to section 'Example job' of 'prokka' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run prokka on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=prokka
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers prokka
prokka --compliant --centre UoN --outdir PRJEB12345 --locustag EHEC --prefix EHEC-Chr1 contigs.fa --cpus 24
prokka-genbank_to_fasta_db Coccus1.gbk Coccus2.gbk Coccus3.gbk Coccus4.gbk > Coccus.faa