parallel_prokka

A wrapper script to run Prokka on multiple assemblies in parallel using GNU parallel.

Usage

./run_prokka.sh --assembly_folder <folder> [--proteins <fasta>] [--jobs <n>] [--cpus <n>]

Options

Flag	Description	Default
--assembly_folder	Folder containing .fasta / .fna assembly files	required
--proteins	Proteins FASTA file for annotation, or none to skip	optional
--jobs, -j	Number of parallel jobs	4
--cpus	CPUs per Prokka run	2

Examples

Run with a custom proteins file:

./run_prokka.sh --assembly_folder assemblies/ --proteins my_proteins.fasta

Run without a proteins file (Prokka default annotation):

./run_prokka.sh --assembly_folder assemblies/
./run_prokka.sh --assembly_folder assemblies/ --proteins none

Run with more parallelism:

./run_prokka.sh --assembly_folder assemblies/ --jobs 8 --cpus 4

Output

Results are written to <assembly_folder>/prokka_out/<sample_name>/.

Dependencies

Install via conda:

conda install -c conda-forge -c bioconda prokka
conda install -c conda-forge parallel

• Prokka — Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014. doi:10.1093/bioinformatics/btu153
• GNU parallel — Tange O. GNU Parallel - The Command-Line Power Tool. USENIX Magazine 2011. doi:10.5281/zenodo.16303