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

• Published in: Genomics (San Diego, Calif.) Vol. 107; no. 5; pp. 189 - 198
• Main Authors: Pereira, Felipe L., Soares, Siomar C., Dorella, Fernanda A., Leal, Carlos A.G., Figueiredo, Henrique C.P.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2016
• Subjects: accuracy; Bacteria; Base Sequence; Chromosome Mapping; comparison; Genome, Bacterial - genetics; Genomics; High-Throughput Nucleotide Sequencing - methods; Multilocus Sequence Typing - methods; NGS; rate indel; Sequence Analysis, DNA; TVC; comparison; Hi-Q; ISP; ION; accuracy; SA20; MiSEQ; Q20; wgMLST; rate indel; InDel; BIGSdb; FNO12; NGS
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2016.03.004

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. •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.