msgr0 / pangebin

Pangebin (WIP)

Pangebin is a nextflow pipeline that permites to run plasmid binning software (Plasbinflow, Gplas for example) on multiple assembly graphs at once, exploiting pangenome graphs capabilities.

Pangebin pipeline takes as input two assembly graphs of a bacterial sample, built from Skesa and Unicycler, builds the augmented pangenome that could be then used as infput for PlasBin-Flow or Gplas.

Requirements

Software required for running the pipeline

• conda/mamba
• nextflow (can be installed via conda -c bioconda)

Input

The input graphs should be named short.gfa.gz for unicycler graphs and skesa.gfa.gz for skesa graphs. Both should be placed into a folder named after the sample_id.

Running the pipeline

nextflow run main.nf -profile mamba --db folder_sample_id --out output will run the pipeline, placing the output gfa into the output folder.

still work-in-progress