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 <strong>samples.csv</strong>. 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.<br> For every weight combination \((a,b,c)\) , we have a file name <em>plasbin_flow_a_b_c_bins.out.</em> PlasBin: <em>plasbin_contig_chains.csv</em>, HyAsP: <em>hyasp_plasmid_contigs.fasta</em>, MOB-recon: <em>mob_recon_contig_report.txt</em>, plasmidSPAdes: <em>plasmidspades_contigs.fasta</em>, gplas: <em>gplas_bins.tab</em>.