Rapid barcoding sequencing kit

Genomic DNA libraries were constructed using AMT Rapid DNA-Seq Kits for Illumina (CISTRO, Guangzhou, China). Fragmentation, end-repair, adaptor ligation with Illumina adapters, size selection with beads, and library DNA amplification were performed according to the manufacturer's instructions. Libraries were assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and a Qubit 3.0 fluorometer (Invitrogen, Waltham, MA, USA). DNA sequencing was performed on the Illumina Nextseq 550 platform with a High Output v2.5 kit (Illumina, San Diego, CA, USA).
Long reads of microbial genomic DNA libraries were prepared using the Rapid Barcoding Sequencing Kit (Nanopore, Oxford, UK) and were sequenced on the Nanopore MinION platform with R9.4.1 flow cells (Nanopore).
Low-quality reads from Illumina sequencing were filtered and removed using Trimmomatic software (v0.39) (38 (link)). Low-quality and short reads from Nanopore sequencing were filtered using Filtlong software (v0.2.0) (https://github.com/rrwick/Filtlong). The filtered Illumina and Nanopore reads were aligned into de novo assembled contigs using Unicycler software (v0.4.8) (39 (link)).

Genomic DNA libraries were constructed using AMT Rapid DNA-Seq Kits for Illumina (CISTRO, Guangzhou, Guangdong, China), with fragmentation, end-repair, adaptor ligation with Illumina adapters, size selection with beads, and library DNA amplification; all methods were performed according to the manufacturer’s instructions. The libraries were assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and a Qubit 3.0 fluorometer (Invitrogen, Carlsbad, CA, USA). DNA sequencing was performed on an Illumina Nextseq 550 platform (Illumina, San Diego, CA, USA) with a High Output v2.5 kit (Illumina). Long reads of microbial genomic DNA libraries were prepared using a Rapid Barcoding Sequencing Kit (Nanopore, Oxford, UK) and sequenced on a Nanopore MinION platform with R9.4.1 flow cells (Nanopore).
Low-quality reads from Illumina sequencing were filtered out using Trimmomatic software (v0.39) (Bolger et al., 2014 (link)). Low-quality and short reads from Nanopore sequencing were filtered using Filtlong software (v0.2.0; https://github.com/rrwick/Filtlong). The filtered Illumina and Nanopore reads were aligned into de novo assembled contigs using Unicycler software (v0.4.8) (Nurk et al., 2013 (link)).