Evaluating the efficacy of the new Ion PGM Hi-Q Sequencing Kit applied to bacterial genomes.
Genomics, 2016/05;107(5):189-98.
Pereira FL[1], Soares SC[2], Dorella FA[3], Leal CA[4], Figueiredo HC[5]
Affiliations
PMID: 27033417
Impact factor: 4.31
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; Genomics; High-Throughput Nucleotide Sequencing; Multilocus Sequence Typing; Sequence Analysis, DNA
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