A hybrid approach for de novo human genome sequence assembly and phasing

Abstract

Despite tremendous progress in genome sequencing, the basic goal of producing a phased (haplotype-resolved) genome sequence with end-to-end contiguity for each chromosome at reasonable cost and effort is still unrealized. In this study, we describe an approach to performing de novo genome assembly and experimental phasing by integrating the data from Illumina short-read sequencing, 10X Genomics linked-read sequencing, and BioNano Genomics genome mapping to yield a high-quality, phased, de novo assembled human genome.

Figure 1

Flowchart depicting genome sequence assembly strategy.

Figure 2. Schematic from the UCSC Genome Browser showing the relative sizes of scaffolds produced during each step of the assembly process, as well as haplotype blocks, for the hybrid scaffold (64 Mb) aligned to the q arm of reference chromosome X

(a) Assembly based on short-read Illumina ata filtered for scaffolds longer than 3 kb; (b) the short-read assembly scaffolded together using barcode information from 10XG data; (c) assembled BNG genome maps; (d) hybrid scaffold produced by merging b and c; (e) barcode-based haplotype blocks for this region; (f) dot plot of the region against reference genome hg38.

Figure 3. Alignment and phasing of the hybrid assembly

(a) Ideograms of the hybrid scaffold assembly aligned to the reference genome hg38, with each colored block representing an assembled scaffold. (b) A 23-Mb phase block (super scaffold 259, aligned to Chr 3 50 Mb-73 Mb) at increasing resolution showing the alleles on the two haplotypes (green vertical line: assembly allele; grey vertical line, alternate allele). Where a green or grey vertical line is not matched with a corresponding mark, the allele is indeterminate on that haplotype.