2.3 Nanopore sequencing and assembly
We prepared DNA using Oxford Nanopore Technologies’ standard ligation
sequencing kit SQK-LSK109DNA. Genomic DNA was size-selected using
high-pass mode (> 20 kb) using a BluePippin BLF7510
cassette (Sage Science). After completion of sequencing, the raw
nanopore sequencing reads were corrected using the program Canu version
1.5 with the parameters ‘minReadLength 3000–min Overlap Length 500’ and
Smartdenovo with the parameters ‘-k 17 -c 1’ (Koren et al., 2017). A
preliminary de novo assembly was constructed using the Nanopore
sequence, then we aligned the Illumina reads to the draft genome
assemblies using BWA-MEM (Li, 2013).