Whole genome sequencing of Bordetella pertussis with MinION Q20 kit and Ilumina MiSeq

For effective disease control, increased accessibility and dissemination of NGS methods should be sought in as many laboratories and hospitals as possible.The characteristics of the most commonly used NGS technique by Ilumina include sequencing of short fragments and parallel elongation of each strand. However, downsides are a high acquisition cost and limitations of profitability to high turnover rates. Nanopore sequencing could be an alternative that reduces the cost and substantially reduces the need for a large number of samples. The initial cost of the instrument is significantly lower than for Ilumina instruments and fewer samples per flow cells can be sequenced cost-effectively. This method produces fragments thousands of base pairs long and thus simplifies whole genome assembly. With the latest updates to flow cells and chemistry, the technology is approaching the quality of comparable short read sequencing. Therefore, it is time for a comprehensive comparison between the two methods for genome assembly and cgMLST analysis of the same isolates. Analysis of the sequencing results should provide interesting insights into the comparability and advantages of each method.