A binning tool to reconstruct viral haplotypes from assembled contigs

Jiao Chen; Jiayu Shang; Jianrong Wang; Yanni Sun

Although a number of contig binning algorithms have been developed (Wu et al., 2014; Alneberg et al., 2014; Kang et al., 2015; Lu et al., 2017; Quince et al., 2017; Luo et al., 2015; Truong et al., 2017) , they all possess limitations in distinguishing contigs from different viral strains of the same species. Most of the existing contig binning tools for microbiome sequencing data are designed for bacteria. These methods usually estimate the bin number by aligning metagenomic data to a pre-established marker gene database, and then assign assembled contigs to different bins using sequence composition information and read coverage levels. For example, MaxBin (Wu et al., 2014) uses both tetranucleotide frequencies and contig coverage levels to assign assembled contigs into different bins.