title: Evaluating the efficacy of the new Ion PGM Hi-Q Sequencing Kit applied to bacterial genomes.
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.
authors.affiliation: 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.
authors.forename: Felipe L
authors.initials: FL
authors.lastname: Pereira
authors.affiliation: AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Brazil. Electronic address: siomars@gmail.com.
authors.forename: Siomar C
authors.initials: SC
authors.lastname: Soares
authors.affiliation: AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Brazil. Electronic address: fernandadorella@gmail.com.
authors.forename: Fernanda A
authors.initials: FA
authors.lastname: Dorella
authors.affiliation: 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.
authors.forename: Carlos A G
authors.initials: CA
authors.lastname: Leal
authors.affiliation: AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Brazil. Electronic address: figueiredoh@yahoo.com.
authors.forename: Henrique C P
authors.initials: HC
authors.lastname: Figueiredo
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D058885:Multilocus Sequence Typing / Q000379:methods*; D017422:Sequence Analysis, DNA
keywords: NGS; accuracy; comparison; rate indel