Evaluating the efficacy of the new Ion PGM Hi-Q Sequencing Kit applied to bacterial genomes

•The novel Ion Torrent Hi-Q Sequencing kit generates data with more quality than the former Ion Torrent Sequencing kit.•Whole-genome MLST is an efficient tool to compare quality assemblies.•Final genome assemblies with Ion Torrent Hi-Q data are closer to the assemblies generated with Illumina MiSEQ.

Benchtop NGS platforms are constantly evolving to follow new advances in genomics. Thus, the manufacturers are making improvements, such as the recent Ion PGM Hi-Q chemistry. We evaluate the efficacy of this new Hi-Q approach by comparing it with the former Ion PGM kit and the Illumina MiSEQ Nextera 3rd version. The Hi-Q chemistry showed improvement on mapping reads, with 49 errors for 10 kbp mapped; in contrast, the former kit had 89 errors. Additionally, there was a reduction of 80% in erroneous variant detection with the Torrent Variant Caller. Also, an enhancement was observed in de novo assembly with a more confident result in whole-genome MLST, with up to 96% of the alleles assembled correctly for both tested microbial genomes. All of these advantages result in a final genome sequence closer to the performance with MiSEQ and will contribute to turn comparative genomic analysis a reliable task.