BinSPreader: refine binning results for fuller MAG reconstruction

Despite the recent advances in high-throughput sequencing, analysis of the metagenome of the whole microbial population still remains a challenge. In particular, the metagenome-assembled genomes (MAGs) are often fragmented due to interspecies repeats, uneven coverage and vastly different strain abundance. MAGs are usually constructed via a dedicated binning process that uses different features of input data in order to cluster contigs that might belong to the same species. This process has some limitations and therefore binners usually discard input contigs that are shorter than several kilobases. Therefore, binning of even simple metagenome assemblies can miss a decent fraction of contigs and resulting MAGs oftentimes do not contain important conservative sequences that might be of great interest of researcher. In this work we present BO_SCPLOWINC_SCPLOWSPO_SCPLOWREADERC_SCPLOW -- a novel binning refiner tool that exploits the assembly graph topology and other connectivity information to refine the existing binning, correct binning errors, propagate binning from longer contigs to shorter contigs and infer contigs belonging to multiple bins. Furthermore, BO_SCPLOWINC_SCPLOWSPO_SCPLOWREADERC_SCPLOW can split input reads in accordance with the resulting binning, predicting reads potentially belonging to multiple MAGs. We show that BO_SCPLOWINC_SCPLOWSPO_SCPLOWREADERC_SCPLOW could effectively complete the binning, increasing the completeness of the bins without sacrificing the purity and could predict contigs belonging to several MAGs.