Nextera xt v2 dna library preparation kit

Whole genome sequencing was performed on 74 strains at the University of Toronto in Canada. DNA was extracted and prepared by using the robotic setup described previously [50 (link)]. The genomes were sequenced using an Illumina GAIIx on 250 bp paired-end libraries in 8-fold multiplexes. The remaining 26 strains were sequenced at SSI in Denmark. DNA was extracted and prepared using Promega Wizard Genomic DNA Purification kit (Promega, Madison, USA) and Nextera XT v2 DNA Library Preparation kit (Illumina, San Diego, USA) according to the manufacturer protocol. Whole genome sequencing was performed using an Illumina MiSeq with 250 bp paired-end technology. All genomes were de novo assembled using CLC Genomic Workbench (Qiagen, USA).

Genomic DNA was extracted from V. cholerae isolates from the primary collection using the Qiagen DNeasy blood and tissue kit. Library construction was completed using the Illumina Nextera XT v.2 DNA library preparation kit. Libraries were sequenced in three Illumina MiSeq runs. Two batches of 24 genomes and one batch of 19 were pooled and sequenced on a MiSeq for 500 cycles per run. Using CLC Genomics Workbench v20, raw reads were filtered by length, trimmed and mapped to the reference genome (V. cholerae O1 El Tor E7946) to identify single-nucleotide variants. Of the 67 isolates, 66 yielded sufficient coverage (>50×) of the V. cholerae genome. We proceeded with these 66 genomes for further analysis. To identify genes not present in the reference genome, contigs were assembled de novo using CLC Genomics Workbench v20.