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PlasmidFinder.md

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PlasmidFinder

PlasmidFinder identifies plasmids in total or partial sequenced isolates of bacteria. Contact Jeevan in slack if you have any issues or further assistance (F. ex. run the tool for multiple isolates).

User Manual

https://bitbucket.org/genomicepidemiology/plasmidfinder/src

For further reading

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4068535/

Here is the EXAMPLE SLURM script for Abel to excute the tool.

Important rules to follow

  • Refer the user manual for all the parameters in the tool
  • Keep your data in /project/nn9305k/
  • Store your resutls also in /project/nn9305k/
  • Execute the script from your home directory
#!/bin/bash
#SBATCH --job-name=DontKillMe
#SBATCH --account=nn9305k
#SBATCH --time=01:00:00
#SBATCH --mem-per-cpu=32G

## Set up job environment:
source /cluster/bin/jobsetup

# Activate Conda environment 
conda activate PlasmidFinder

# Database location
DB="/work/projects/nn9305k/src/PlasmidFinder/PlasmidFinder_DB/plasmidfinder_db/"

# Note: Dont need to mention the BLAST location
python /work/projects/nn9305k/src/PlasmidFinder/plasmidfinder/plasmidfinder.py -p $DB -i input_file -o output_file

# deactivate Conda environment 
conda deactivate