KPC Plasmid analysis

• this repository was used in this work:

Brandt, C. et al. Assessing genetic diversity and similarity of 435 KPC-carrying plasmids. Scientific Reports 9, 11223 (2019) https://doi.org/10.1038/s41598-019-47758-5

• TLDR: KPC plasmid clustering workflow via Nextflow
• workflow is only tested and intended for KPC-plasmids

Installation

Dependencies

• Nextflow
• Docker

A example installation for Docker and Nextflow:

# NEXTFLOW
# java runtime for nextflow, test if installed via 'java -version'
  apt install openjdk-11-jre
# install nextflow
  curl -s https://get.nextflow.io | bash
# move 'nextflow' to a $PATH location, or add 'nextflow' to $PATH
  mv nextflow /usr/local/bin

# DOCKER
# Install via https://docs.docker.com/install/ (most recent) or:
  apt install docker-ce
# Add docker group to $USER
  sudo usermod -a -G docker $USER
# restart terminal or reboot if neccessary

Usage

nextflow run replikation/plasmid_analysis --input list_of_accession_numbers.txt

• reproduce the KPC clustering

# clone the git and navigate into
git clone https://github.com/replikation/plasmid_analysis.git
cd plasmid_analysis
# execute Nextflow using the Accessionlist of May
nextflow run main.nf --input Accessionlist/Accessionlist_KPC_nt_archive_all_May_2019.txt --cpus 8      

• Accessionlist_KPC_nt_archive_all_May_2019.txt is given as a example
• feel free to use another accession list:
  • only one accession number per line
  • no headers
• results are stored in cluster_results

• a simplified result collection for KPC-plasmids can be used via bash collect_results.sh

Resume

• nextflow is able to resume a run
• add -resume to the last nextflow command

help message

• nextflow run main.nf --help

Usage:

nextflow run main.nf --input Accession_list.txt

--input       a list of accession numbers, one accession number per line, no headers
                e.g. do a 'cut -f2' on a blastn query with '-outfmt6'

Options:
--cpus        max cores [default 8]

Results are stored in cluster_results/

Additional Information

• Dockerfiles created for this workflow are located under Dockerfiles/
• the work folder can be removed afterwards

prokka

• prokka uses a ncbi dependency tbl2asn which may expire at some point see here or here
  • this workflow will use prokka:latest instead of a fixed version to avoid this issue in the future