Assembly and correction of the Genome
De novo assembly was performed on the basis of PacBio long reads using
FALCON v0.3.0 (https://github.com/PacificBiosciences/falcon). Error
correction and pre-assembly were initially performed following the
FALCON pipeline, with a length_cutoff of 28 kb and a length_cutoff_pr
of 27 kb chosen for the assembly step. The draft assembly was corrected
using Arrow, based on the mapping results of the PacBio reads to the
assembled genome when following the BLASR pipeline (Chaisson & Tesler,
2012). Next, all filtered Illumina reads were mapped to the corrected
contigs using BWA-mem (H. Li & Durbin, 2009), to polish the genome for
3-rounds of Pilon iteratively (Walker et al., 2014).