https://github.com/ssi-dk/prokka_roary_toolbox
Scripts for running prokka and roary on calc.
https://github.com/ssi-dk/prokka_roary_toolbox
Last synced: 9 months ago
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Scripts for running prokka and roary on calc.
- Host: GitHub
- URL: https://github.com/ssi-dk/prokka_roary_toolbox
- Owner: ssi-dk
- Created: 2022-05-31T10:33:13.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-11-10T09:28:45.000Z (about 3 years ago)
- Last Synced: 2025-01-11T09:44:35.316Z (10 months ago)
- Language: Python
- Size: 18.6 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Prokka/Roary toolbox
Scripts for easily running prokka and roary on calc.
## Run Prokka
### Input
A directory containing genomic assemblies (.fa, .fna, .fasta)
### Output
A directory for each input-fasta file containing annotated output in a range of different formats (gbk, gff, faa, fna)
### Usage
*source activate env_prokka*
*run_prokka_on_folder.py assemblies_directory prokka_out project*
## Run Roary
### Input
The output directory from prokka. Roary uses the input files from these which are first gathered and renamed for easier handling
### Usage
*gather_gff_from_prokka.py prokka_out roary_in*
*source activate env_prokka*
*sbatch -D . -c 8 --mem=24G --time=48:00:00 -J "Roary" -p daytime --wrap="roary -e --mafft -p 8 –f roary_out roary_in/\*.gff"*
## What does it do?
Prokka does genome annotation on individual fasta files, roary compares gene content between isolates and outputs a range of different plots and tables to be analyzed.
## Links
### Prokka
https://github.com/tseemann/prokka
### Roary
https://sanger-pathogens.github.io/Roary/
### Blast suite
https://www.ncbi.nlm.nih.gov/books/NBK279690/