A binning tool to reconstruct viral haplotypes from assembled contigs

Jiao Chen; Jiayu Shang; Jianrong Wang; Yanni Sun

In this experiment, we applied VirBin to a mock HIV quasispecies data set (SRR961514), sequenced from the mix of five HIV-1 strains (89.6, . CC-BY-NC-ND 4.0 International license The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a . https://doi.org/10.1101/704288 doi: bioRxiv preprint HXB2, JRCSF, NL43, YU2) with Illumina MiSeq sequencing technology (Di Giallonardo et al., 2014) . This data set contains 1,429,988 (250 bp) of reads that cover the five strains to 20,000x. The raw data set was preprocessed with FaQCs/1.3 (Lo and Chain, 2014) and Trimmomatic (Bolger et al., 2014) to trim and filter low-quality reads or adapters. The remaining reads were then error-corrected with Karect (Allam et al., 2015) . After pre-processing, 774,044 reads were left. By mapping pre-processed reads to the available 5 reference genomes by bowtie2, we were able to estimate the abundance for each haplotype as shown in Fig. 8 .