The Francisella tularensis sp. holarctica strain FSC200 [11 ], and a genetic near neighbor Francisella hispaniensis strain FSC454 were chosen as an example dataset in case 1 to 3 of this study. The genome assembly of FSC200 is available as RefSeq assembly accesssion GCF_000168775.2 and genome assembly of FSC454 as RefSeq assembly accession GCF_001885235.1. Previously, generated Illumina HiSeq reads of FSC200 are available as NCBI SRA run SRR518502. This latter dataset was subsampled down to an estimated coverage of 100X (1.9 M 100 bp reads) for use in case 1, subsampling was performed with seqtk [12 ](v. 1.2-r94, installed through bioconda [13 ]).
New sequencing libraries were prepared from DNA extractions of the two bacterial strains using the SQK-LSK108 Ligation Sequencing Kit according to the manufacturer’s specifications and then sequenced using a FLO-MIN107 MinION flow cell (Oxford Nanopore Technologies, UK). MinION sequence reads for FSC200 are available as NCBI SRA run SRR9290761, and for FSC454 as NCBI SRA run SRR9290851. Subsampling down to 50,000 from 132,259 MinION reads for FSC200 and 15,000 from 15,757 MinION reads for FSC454 was performed with a custom script, and the sequences were trimmed to a maximum length of 3000 bp as well as being sorted by length to increase classification speed.
New sequencing libraries were prepared from DNA extractions of the two bacterial strains using the SQK-LSK108 Ligation Sequencing Kit according to the manufacturer’s specifications and then sequenced using a FLO-MIN107 MinION flow cell (Oxford Nanopore Technologies, UK). MinION sequence reads for FSC200 are available as NCBI SRA run SRR9290761, and for FSC454 as NCBI SRA run SRR9290851. Subsampling down to 50,000 from 132,259 MinION reads for FSC200 and 15,000 from 15,757 MinION reads for FSC454 was performed with a custom script, and the sequences were trimmed to a maximum length of 3000 bp as well as being sorted by length to increase classification speed.