RasmussenLab/PlasMAAG: PlasMAAG 0.1.0

This upload provides everything needed to run the PlasMAAG (https://www.biorxiv.org/content/10.1101/2025.02.26.640269v2) workflow with example input files for a specific version. plasmaag_repo.tar.gz contains a snapshot of the PlasMAAG at version 0.1.0, ensuring consistency and reproducibility. It serves the same purpose as cloning the repository, but without the risk of future changes. input_data.tar.gz includes all input files required to perform a test run of the PlasMAAG workflow:

• read_and_assembly_file.txt # Contains paths for the paired reads, and assemblies, per sample 
• extracted_reads_clean_sample_{0,1}_{fw,rv}.fq # Forward and reverse read files per sample 
• spades{0,1} # Assembly directories, containing the output of running metaSPAdes on the paired reads per sample:
  • assembly_graph_after_simplification.gfa # simplified assembly graphs
  • contigs.fasta # fasta file containing the assembled contigs
  • contigs.paths # metadata file with information related to the contigs and assembly graphs 

To install PlasMAAG test version, first download plasmaag_repo.tar.gz and then:

tar -xvzf plasmaag_repo.tar.gz # decompress directory

conda env create -n PlasMAAG_zenodo --file=PlasMAAG/envs/PlasMAAG.yaml

To use the program first activate the conda environment:

conda activate PlasMAAG_zenodo

Decompress inputs:

tar -xvzf input_data.tar.gz # decompress inputs

cd input_data

And then run the pipeline testrun:

PlasMAAG --reads_and_assembly_dir read_and_assembly_file.txt --output testrun -t 8--vamb_arguments '-o C -e 200 -q 25 75 150 --seed 1'

Once the workflow finishes, several files and folders will be generated within the testrun directory, thoroughly described here. Final products of the pipeline can be found in the testrun/results directory, containing:

candidate_plasmids.tsv # The candidate plasmids
candidate_genomes.tsv # The candidate chromosomes
candidate_plasmids # Directory with the candidate plasmids fasta files
candidate_genomes # Directory with the candidate chromosomes fasta files
scores.tsv # The aggregated scores for each plasmid and genome cluster

More information can be found in PlasMAAG're repository. Please remember that the PlasMAAG command has been modified for the testrun. So, when running PlasMAAG on real samples, please remove the --vamb_arguments '-o C -e 200 -q 25 75 150 --seed 1'.