DNA for Illumina sequencing was prepared using the CTAB method described elsewhere [21] . Genomic DNA was isolated from freshly grown strains using QIAamp DNA minikit (Qiagen, Germany) following the manufacturer’s instructions and was quantified using Qubit fluorometer (Life Technologies, USA). Sequencing libraries were prepped using Illumina Nextera XT DNA sample preparation kit (Illumina, USA) and were sequenced on a MiSeq Illumina platform using MiSeq v3 chemistry. Strains from Norway were sequenced at the Norwegian Sequencing Centre, whereas Indian isolates were sequenced at All India Institute of Medical Sciences. Output data files were de-multiplexed and transformed into fastq files with Casava v.1.8.2 (Illumina Inc, USA).
Raw sequencing data were filtered using Trimmomatic v 0.38 [22] (link). Adapters were removed, and low-quality read ends with an average Phred quality score <15 within a 4-bp window were trimmed. Reads with an average Phred quality score <15 and/or shorter than 36 bp after adapter removal and trimming were discarded.
Six isolates were additionally sequenced on the MinION platform (Oxford Nanopore Technology, UK) following a previously published protocol [6] (link).
Raw sequencing data were filtered using Trimmomatic v 0.38 [22] (link). Adapters were removed, and low-quality read ends with an average Phred quality score <15 within a 4-bp window were trimmed. Reads with an average Phred quality score <15 and/or shorter than 36 bp after adapter removal and trimming were discarded.
Six isolates were additionally sequenced on the MinION platform (Oxford Nanopore Technology, UK) following a previously published protocol [6] (link).
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