Evaluating the efficacy of the new Ion PGM Hi-Q Sequencing Kit applied to bacterial genomes
2016
Pereira, Felipe L. | Soares, Siomar C. | Dorella, Fernanda A. | Leal, Carlos A.G. | Figueiredo, Henrique C.P.
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 10kbp 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.
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