Nanopore Guided Assembly of Segmental Duplications near Telomeres

Abstract

Human subtelomere regions are highly enriched in large segmental duplications and structural variants, leading to many gaps and misassemblies in these regions. We develop a novel method, NPGREAT (NanoPore Guided REgional Assembly Tool), which combines Nanopore ultralong read datasets and short-read assemblies derived from 10x linked-reads to efficiently assemble these subtelomere regions into a single continuous sequence. We show that with the use of ultralong Nanopore reads as a guide, the highly accurate shorter linked-read sequence contigs are correctly oriented, ordered, spaced and extended. In the rare cases where a linked-read sequence contig contains inaccurately assembled segments, the use of Nanopore reads allows for detection and correction of this error. We tested NPGREAT on four representative subtelomeres of the NA12878 human genome (10p, 16p, 19q and 20p). The results demonstrate that the final computed assembly of each subtelomere is accurate and complete.

Keywords: genome assembly; linked reads sequencing; nanopore; segmental duplications; subtelomere.

Figure 1.

The assembly algorithm. Input: The selected ultralong Nanopore reads (NReads), the selected short REXTAL contigs (RContigs) and the chromosome number (chrID). Output: The assembled sequence (sequence).

Figure 2.

Definition of a gap or an overlap between two REXTAL contigs. The red color designates the border local alignments of the neighboring REXTAL contigs and the blue color shows the Nanopore read’s alignment with the two contigs. The green color and prime letters constitute REXTAL contigs extended in repeat-masked parts of Nanopore reads. The purple color defines the bridging region. (a) A gap between the two contigs. (b) An overlap between two contigs. (c) Possible overlap, further investigation required.

Figure 3.

10p Subtelomere region comparison with REXTAL and HG38.

Figure 4.

16p Subtelomere region comparison with REXTAL and HG38.