gDNA sequencing of Salmonella enterica 4/74: late stationary phase growth phase in L-broth (16h of growth) biorep
Nanopore sequencing libraries were prepared according to the genomic DNA Ligation Sequencing Kit V14 (SQK-NBD114-24) protocol (Oxford Nanopore Technologies, Oxford Science Park, OX4 4DQ, UK). Prepared libraries were loaded on MinION flow cells (R10.4) and sequenced with the MinION Mk1B device using Kit 14 chemistry and MinKNOW v23.07.8 (Oxford Nanopore Technologies, Oxford Science Park, OX4 4DQ, UK). Basecalling of raw Oxford Nanopore signal data was performed using Dorado v0.8.3 with the super accuracy (sup) model dna_r10.4.1_e8.2_400bps_sup@v5.0.0 (5 kHz). Methylation calling for N6-methyladenine (m6A) and N4/N5-methylcytosine (m4C/m5C) was conducted using the corresponding modified base models, dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v2 and dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v2. Demultiplexing was performed using the dorado demux command with the kit name specified as --kit-name SQK-NBD114-24.