Application notes and literature
Ion Torrent sequencing is cited in more than 900 peer-reviewed publications on microbial sequencing for bacterial and viral typing research, metagenomics, and discovery of unknown microorganisms.
Antwerpen MH, (2015) Rapid High Resolution Genotyping of Francisella tularensis by Whole Genome Sequence Comparison of Annotated Genes (“MLST+”). PLoS ONE 10(4): e0123298. doi:10.1371/journal.pone.0123298
Ion Torrent Personal Genome Machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information. J Clin Microbiol JCM.00038-12 [pii];10.1128/JCM.00038-12 [doi]. Vogel U, et al. (2012)
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. JCM.06094-11 [pii];10.1128/JCM.06094-11 [doi]. Larsen et al. (2012).
Bacterial typing research informatics solutions
Torrent Suite Software provides the tools that take you from raw sequence data to informative results, including optimized signal processing, base calling, sequence alignment, and variant analysis. Post run, sequencing data are available for download with a simple right-click. Reports are also easily browsed, with expandable analysis plots and straightforward tables that summarize key results to help ensure that sequencing runs are of high quality.
The Torrent Browser Plugin Store provides Torrent Suite Software users a simple, one-stop location to browse and quickly install any plugin of interest to expand the analysis capabilities of their Torrent Server. Plugins are available for microbial resequencing (Alignment, PathFinder and PathogenDetector), de novo assembly (AssemblerSPAdes), and other applications.
Specific workflows for bacterial and viral typing in third-party software packages, such as the Ridom SeqSphere+ software package, automate downstream analysis. SeqSphere+ enables your lab to carry out whole genome microbial typing (MLST+), traditional MLST, or 16S rDNA sequencing projects. This software is designed for individual or distributed work-groups (client/server model) to enable easy data sharing.
Learn more about how this software can simplify your data analysis.
For Research Use Only. Not for use in diagnostic procedures.
The Ion Plus Fragment Library Kit or Ion Xpress™ Plus Fragment Library kit provides low-cost sample preparation in as little as 2 hours for gDNA and amplicon libraries.
The Ion Chef™ System® provides simple, high-throughput template preparation with only minutes of hands-on time. The Ion OneTouch™ 2 System provides simple, 15-minute template preparation for 400 or 200 bp sequencing runs.
The Ion S5™ System enables rapid sequencing with 400 or 200 bp sequencing in just 4 hours or 2.5 hours, respectively, on either the Ion 520™ Chip or the Ion 530™ Chip.
Primary data analysis is performed using Torrent Suite™ Software. The Ridom™ SeqSphere+ software package provides a follow-on solution for bacterial typing.
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50(4):1355–1361. Larsen MV, Cosentino S, Rasmussen S, et al. (2012)
Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information. J Clin Microbiol 50(6):1889–1894. Vogel U, Szczepanowski R, Claus H, et al. (2012)
J Bacteriol 194(10):2759–2760. Amaral GR, Silva BS, Santos EO, et al. (2012)
Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities. J Bacteriol 194(16):4461–4462. Kostka JE, Green SJ, Rishishwar L, et al. (2012)
Next-generation Ion Torrent sequencing of drug resistance mutations in Mycobacterium tuberculosis strains. J Clin Microbiol 50(12)3831–3837. Daum LT, Rodriguez JD, Worthy SA, et al. (2012)
Draft genome sequence of Staphylococcus vitulinus F1028, a strain isolated from a block of fermented soybean. J Bacteriol 194(21):5961–5962. Nam YD, Chung WH, Seo MJ, et al. (2012)
Molecular evidence for interspecies transmission of H3N2pM/H3N2v influenza A viruses at an Ohio agricultural fair, July 2012. Emerg Microbes and Infec 1: e33. 10. Bowman AS, Sreevatsan S, Killian ML, et al. (2012
Isolation of a novel swine influenza virus from Oklahoma in 2011 which is distantly related to human influenza C viruses. PLoS Pathog 9(2):e1003176. Hause BM, Ducatez M, Collin EA, et al. (2013)
Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol [Epub ahead of print]. Sherry NL, Porter JL, Seemann T, et al. (2013)