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

<p>PlasBin-flow is a method&nbsp;for detecting plasmid contigs bins from the assembly graph for a given bacterial sample. The method&nbsp;is&nbsp;based on a Mixed-Integer Linear Programming (MILP) formulation.</p> <p>The data shared consists of output files of PlasBin-flow as well as those&nbsp;of&nbsp;5 other&nbsp;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>.&nbsp;&nbsp;&nbsp;</p> <p>The output folder contains one folder per sample. Each sample folder contains the following files:&nbsp;&nbsp;</p> <ul> <li>PlasBin-flow was executed using 7 different weight combinations for the objective function of the MILP.<br> For every&nbsp;weight combination <span class="math-tex">\((a,b,c)\)</span>&nbsp;, we have a file name <em>plasbin_flow_a_b_c_bins.out.</em></li> <li>PlasBin: <em>plasbin_contig_chains.csv</em>,</li> <li>HyAsP: <em>hyasp_plasmid_contigs.fasta</em>,</li> <li>MOB-recon: <em>mob_recon_contig_report.txt</em>,</li> <li>plasmidSPAdes: <em>plasmidspades_contigs.fasta</em>,</li> <li>gplas: <em>gplas_bins.tab</em>.</li> </ul> <p>&nbsp;</p> <p>&nbsp;</p>