simulate_metagenomes

Code modified from https://github.com/fmaguire/MAG_gi_plasmid_analysis focusing on simulating metagenomes

This method helps ensure that genomes carrying plasmids have realistic copy-number dynamics instead of the genome and plasmid sequences being present at 1:1 ratios (which is probably unrealistic).

Quickstart

Clone repo
Ensure requirements are met (see env.yml for conda environment specs)
Decompress sequence data
Run simulate_metagenome.py with desired parameters
- this script takes 5 positional arguments:
  - 1 = seed
  - 2 = metadata path
  - 3 = seq_data directory
  - 4 = output directory
  - 5 = coverage (original script used 3.9)

git clone https://github.com/Jtrachsel/simulate_metagenomes.git 
cd simulate_metagenomes 
conda env create -n magsim_lite --file environment.yml  
conda activate magsim_lite  
tar -xzvf seq_data/sequences.tar.gz  
./simulate_metagenome.py 1 original_community.tsv ./seq_data/ ./output/ 3.9

Notes

You can change the community proflle by adding or removing organisms both in the metadata (original_community.tsv) and the seq_dat folder. You will need to provide a plasmid/chromosome classification for each contig, and match the directory structure found in the seq_data directory.
Probably best to only use complete genomes.