2015
DOI: 10.1128/aem.00111-15
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Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH

Abstract: cThe sequencing chips and kits of the Ion Torrent Personal Genome Machine (PGM), which employs semiconductor technology to measure pH changes in polymerization events, have recently been upgraded. The quality of PGM sequences has not been reassessed, and results have not been compared in the context of a gene-targeted microbial ecology study. To address this, we compared sequence profiles across available PGM chips and chemistries and with 454 pyrosequencing data by determining error types and rates and diazot… Show more

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Cited by 27 publications
(22 citation statements)
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References 34 publications
(39 reference statements)
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“…In comparison to the FunGene tool, TaxADivA meets particular needs, such as filtering of cluster IV/V sequences (see below) and trimming of highly degenerate primer sequences. Trimming of primer sequences may fail during quality control (33), likely due to the extreme degeneracy of nifH primers, and thus we adapted the primer trimming function in the TaxADivA script to trim a specified number of bases off the flanking ends of the amplicon.…”
Section: Discussionmentioning
confidence: 99%
“…In comparison to the FunGene tool, TaxADivA meets particular needs, such as filtering of cluster IV/V sequences (see below) and trimming of highly degenerate primer sequences. Trimming of primer sequences may fail during quality control (33), likely due to the extreme degeneracy of nifH primers, and thus we adapted the primer trimming function in the TaxADivA script to trim a specified number of bases off the flanking ends of the amplicon.…”
Section: Discussionmentioning
confidence: 99%
“…PEPPA thus supports an analysis of the accumulation of pseudogenes with time by individual bacterial lineages, and might be useful for studies concerning the importance of pseudogenes for potential adaptations to new environments. Draft genome assemblies based on 454 or IonTorrent sequencing include elevated numbers of single-base insertions and deletions due to inaccurate sequencing (Shao et al 2013;Zhang et al 2015). Including such genomes in an analysis reduces the quality of the pan-genome for all state of the art pipelines.…”
Section: Effects Of Internal Annotations By Peppa Our Analyses Of 15mentioning
confidence: 99%
“…Current NGS platforms include GS FLX Titanium/GS FLX Junior from Roche, SOLiD and Ion Torrent platforms from Life Sciences, the PacBio RS II from Pacific Biosciences, and Genome Analyzer/HiSeq/MiSeq/NextSeq from Illumina. Owing to the specifics of enzymology, chemistry, high-resolution optics, hardware, and software, each platform differs in the types of sequencing errors (i.e., artifacts) (reviewed in [ 33 35 ]) and quantity of data produced (for detailed methodology, see [ 1 , 3 5 , 36 44 ]). Most NGS projects sequence genomes via the assembly of short (60–150 base pair or bp) reads.…”
Section: Introductionmentioning
confidence: 99%