PacBio Sequel and Illumina NovaSeq PE150 platforms were used for whole genome sequencing at the Beijing Novogene Bioinformatics Technology Co., Ltd. (Beijing, China) Library for single-molecule real-time (SMRT) sequencing in the PacBio Sequel platform was constructed with an insert size of 20 kb using the SMRTbell™ Template kit version 1.0. The library quality was assessed by Qubit® 2.0 Fluorometer (Thermo Scientific) and the insert fragment size was detected by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Regarding the Illumina NovaSeq PE150 platform, sequencing library of 350 bp was generated from 1 μg DNA using NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) following manufacturer’s recommendation. The library was analyzed for size distribution by Agilent 2100 Bioanalyzer (Agilent Technologies).
After filtering low-quality reads (less than 500 bp), the clean data from the PacBio Sequel platform were preliminary assembled using SMRT Link version 5.0.1. The long reads were selected (more than 6 kb) as the seed sequence, and the other shorter reads were aligned to the seed sequence using BLASR version 5.3.5 [24 (link)]. Finally, the arrow algorithm was used to correct and count the variant sites in the initial genome sequence using the variant Caller module of the SMRT Link.
Regarding the Illumina NovaSeq PE150 platform, sequencing library of 350 bp was generated from 1 μg DNA using NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) following manufacturer’s recommendation. The library was analyzed for size distribution by Agilent 2100 Bioanalyzer (Agilent Technologies).
After filtering low-quality reads (less than 500 bp), the clean data from the PacBio Sequel platform were preliminary assembled using SMRT Link version 5.0.1. The long reads were selected (more than 6 kb) as the seed sequence, and the other shorter reads were aligned to the seed sequence using BLASR version 5.3.5 [24 (link)]. Finally, the arrow algorithm was used to correct and count the variant sites in the initial genome sequence using the variant Caller module of the SMRT Link.
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