Combining Nanopore Sequencing and Conformation Capture for the Reconstruction of Complete Chromosomes

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. Recently, several groups have sequenced eukaryotic genomes using the Oxford Nanopore MinION, including 60X of a human genome. We leveraged Canu, a complete reworking of Celera Assembler specifically designed for noisy single-molecule sequences, to assemble these datasets. Combining the assembly with existing HiC data, Canu’s graphical outputs identify assembly errors and guide scaffolding. The resulting scaffolds are highly contiguous with several chromosomes assembled into single scaffolds. For remaining assembly structures that cannot be linearly represented, Canu provides graphical assembly outputs for targeted analysis. We conclude that the Oxford Nanopore MinION is now applicable to eukaryotic genome assembly. These advances will help democratize sequencing due to low instrument cost and improved scaffolding will enable routine high-quality genomes.

Canu source code and pre-compiled binaries are freely available under a GPLv2 license from https://github.com/marbl/canu.

The NA12878 sequence data used in this research was generated by the Nanopore WGS Consortium the University of Oxford's Wellcome Trust Centre for Human Genetics and Genomics plc using Oxford Nanopore Technologies' MinION technology.