ANT_H3_plasmids_genomics

This repo includes data and code used for the comparative genomic analysis of Psychrobacter sp. ANT_H3 plasmids compared with other plasmids from Psychrobacter spp. described in the article "Structure and functions of a multireplicon genome of Antarctic Psychrobacter sp. ANT_H3 – characterization of the genetic modules suitable for the construction of the plasmid-vectors for cold-active bacteria".

How to run the analysis

1. Create conda environment with all required software

You can either use the provided YAML file or install all the required tools by yourself

# using conda
conda env create --file anth3_env.yml
# or mamba which resolves dependencies more efficiently
mamba env create --file anth3_env.yml

2. Activate the conda env

conda activate anth3

3. Run the BASH script where all the commands have comments

bash run_analysis.sh

4. All output files will be in analysis directory.

• analysis/circos/ANT_H3.nucl.svg file was further processed to create panel A in Figure 2.
• analysis/network/net_noG_simple.graphml file was opened with Gephi v0.9.7 and further filtered and processed manually to generate panel B in Figure 2.