Pangebin Pipeline (WIP)

Pangebin is a collection of methods aimed at performing the task of "plasmid binning" on a bacterial sample, exploiting a pangenome construction on a pair of assembly graph, running a modified version of @chauvec 's Plasbin-Flow and, lastly,

Requirements

• nextflow
• PBF requirements:

using conda using docker/podman, a single docker image prebuilt for this task using singularity, a single singularity image prebuilt for this task

using it locally (we assume that every requirement is satisfied locally)

Running the pipeline

1. pangenome construction --profile step1
   input: u.gfa.gz, s.gfa.gz
   output: psm.gfa.gz

2. model + binning --profile step2
   input: psm.gfa.gz
   output: bins.tsv

3. evaluation --profile step3
   input: psm.gfa.gz, bins.tsv, ID
   output: eval.labeling.txt, eval.binning.txt

• whole pipeline --profile all (or no profile)
  input: u.gfa.gz, s.gfa.gz, ID
  output: pangenome, bins, eval.labeling.txt, eval.binning.txt\

Assembly graphs and Pangenome construction

The input is composed by:

• unicycler and skesa graphs in .gfa or .gfagz format
• pangenome graph built with nf-core Pangenome (PGGB).

Plasbin-Flow + pangenome

tbd

Output Bins

tbd