Tutorial to reproduce data presented in the paper: PCNE: a tool for plasmid copy number estimation.
All the required files (reads, assemblies ...) are available here: https://doi.org/10.5281/zenodo.17550873
The following tools and relative dependencies are required:
All the analyses have been performed in a separate conda env
conda create -n pcne -c bioconda pcne
conda create -n mobsuite -c bioconda mob_suite
conda create -n platon -c bioconda platon
conda create -n shovill -c bioconda shovill
conda create -n art -c bioconda art
conda create -n iss -c bioconda insilicoseq
conda create -n abricate -c bioconda abricate
For further details, look at the respective documentation pages.
All scripts require 5 CPUs and 16 GB of RAM maximum.
Go to the working directory and put the chromosome and plasmid files in it.
In the working directory, execute the script art.sh and iss.sh
In the working directory, execute the script pcne_50x.sh.
In the working directory, execute the script shovill.sh
First, download the platon database following instructions, and put it in the working directory.
In the working directory, execute the script pcne_platon.sh
In the working directory, execute the script pcne_mobsuite.sh
To reproduce real data, 5 cpus and 32 GB of memory are required
Download filtered reads directly from https://doi.org/10.5281/zenodo.17550873, or in alternative you can use prefetch following the instructions.
WGS reads are deposited at SRA archive under BioProject PRJNA1044738
Once downloaded, rename the reads as their sample name (ex. EM4N2)
To filter reads use FastP setting quality filter -q 30
Put the reads in a folder named "Real_data_reads", and from working directory launch real_data_assembly.sh
From working directory run platon_real_data.sh
From working directory run pcne_real_data.sh
To reproduce real data, 5 cpus and 32 GB of memory are required
Download filtered reads directly from https://doi.org/10.5281/zenodo.17550873, or in alternative raw reads from SRA.
Once downloaded, rename the reads as their sample name (KP_01, ...)
To filter reads use FastP setting quality filter -q 30
Put reads in a folder named "Case_study_reads", and from working directory launch case_study_shovill.sh.
From working directory run case_study_mobsuite.sh
From working directory run case_study_abricate.sh
From working directory run case_study_pcne.sh