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

Felipe L Pereira; Siomar C Soares; Fernanda A Dorella; Carlos A G Leal; Henrique C P Figueiredo

doi:10.1016/j.ygeno.2016.03.004

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

Genomics. 2016 May;107(5):189-98. doi: 10.1016/j.ygeno.2016.03.004. Epub 2016 Mar 24.

Authors

Felipe L Pereira¹, Siomar C Soares², Fernanda A Dorella³, Carlos A G Leal⁴, Henrique C P Figueiredo⁵

Affiliations

¹ AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Brazil. Electronic address: felipe@flpsw.com.br.
² AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Brazil. Electronic address: siomars@gmail.com.
³ AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Brazil. Electronic address: fernandadorella@gmail.com.
⁴ AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Brazil. Electronic address: carlosleal@vet.ufmg.br.
⁵ AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Brazil. Electronic address: figueiredoh@yahoo.com.

PMID: 27033417
DOI: 10.1016/j.ygeno.2016.03.004

Abstract

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.

Keywords: NGS; accuracy; comparison; rate indel.

MeSH terms

Base Sequence
Chromosome Mapping
Genome, Bacterial / genetics*
Genomics
High-Throughput Nucleotide Sequencing / methods*
Multilocus Sequence Typing / methods*
Sequence Analysis, DNA