Genome size estimation and genome assembly
The Kmer-based method of the Illumina short read data was used to
analyze the genome survey to estimate the genome size, heterozygosity,
and repeat content of the burbot genome (Liu et al., 2013). The
NextDenovo package (https://github.com/Nextomics/NextDenovo) was
performed to assemble the burbot genome with PacBio long reads by using
the following parameters: parallel_jobs, 300; seed_cutoff, 15,000;
pa_correction, 320; and random_round, 100. To correct the random
sequencing errors in the NextDenovo output, two steps of genome sequence
polishing were applied. The arrow was used to polish the genome by using
the long sequencing data (Chin et al., 2013), and two rounds of
polishing using Illumina short reads were then applied with Pilon
(Walker et al., 2014).