Rapid sequencing kit sqk rad001

Library preparation was performed using a SQK-NSK007 Nano Sequencing Kit R9 version (Oxford Nanopore Technologies, Oxford, UK) and Rapid Sequencing Kit SQK-RAD001 (Oxford Nanopore Technologies, Oxford, UK) using 1 µg and 200 ng amplicon DNA, for 2D amplicon sequencing and rapid 1D sequencing, respectively, according to the manufacturer’s protocols. MinION sequencing was performed using the MinION Mk1 b sequencer and FLO-MIN104 flow cells. Raw data (fast5 files) were obtained using MinKNOW software ver. 1.0.2 (Oxford Nanopore Technologies, Oxford, UK).

MinION 1D sequencing was performed using the Rapid Sequencing Kit SQK-RAD001 (Oxford Nanopore Technologies, Oxford, UK) with 200 ng of amplicon DNA. The MinION Mk1 b sequencer and FLO-MIN105 flow cell were used for sequencing. We used MinKNOW software ver. 1.1.17 for this sequencing run. This version allows local base-calling for 1D sequencing data using the protocol script NC_48Hr_Sequencing_Run_FLO_MIN104_plus_1D_Basecalling, to minimise analysis time. Bacterial identification was performed using BLAST and Centrifuge, as described above, and results were compared between the two sequencers. IonPGM sequencing using the same DNA was performed using the above-mentioned 16S Metagenomics Kit (Thermo Fisher Scientific, MA, USA).