PlasBin-flow: A flow-based MILP algorithm for plasmid contigs binning

PlasBin-flow is a method for detecting plasmid contigs bins from the assembly graph for a given bacterial sample. The method is based on a Mixed-Integer Linear Programming (MILP) formulation.

The data shared consists of output files of PlasBin-flow as well as those of 5 other plasmid binning methods, namely, PlasBin, HyAsP, MOB-recon, plasmidSPAdes and gplas for 66 test samples. Details about each sample have been provided in the file samples.csv.   

The output folder contains one folder per sample. Each sample folder contains the following files:  

• PlasBin-flow was executed using 7 different weight combinations for the objective function of the MILP.
  For every weight combination \((a,b,c)\) , we have a file name plasbin_flow_a_b_c_bins.out.
• PlasBin: plasbin_contig_chains.csv,
• HyAsP: hyasp_plasmid_contigs.fasta,
• MOB-recon: mob_recon_contig_report.txt,
• plasmidSPAdes: plasmidspades_contigs.fasta,
• gplas: gplas_bins.tab.