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replikation/prokka

By replikation

•Updated over 6 years ago

FROM: https://github.com/tseemann/prokka

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replikation/prokka repository overview

⁠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

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

Tag summary

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Image

Digest

Size

795.3 MB

Last updated

over 6 years ago

docker pull replikation/prokka