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 Ion S5 Infectious Disease application note

Application notes & publications
Read application notes and peer-reviewed publications to learn how the Ion Torrent sequencing systems have been used for bacterial and viral typing research.

Data set
Download a data set generated on the Ion PGM™ System and see the results for yourself.


Informatics solutions
Learn about bacterial identification informatics solutions for the fastest way to get to your biological results.

Bacterial typing workflow for the Ion S5 System
1 Construct

The Ion Plus Fragment Library Kit or Ion Xpress™ Plus Fragment Library kit provides low-cost sample preparation in as little as 2 hours...Read more

2 Prepare

The Ion Chef™ System† provides simple, high-throughput template preparation with only minutes of hands-on time....Read more

3 Run
Ion S5

The Ion S5 System enables rapid sequencing with 400 or 200 bp sequencing in just 4 hours...Read more

4 Analyze

Primary data analysis is performed using Torrent Suite™ Software. The Ridom™ SeqSphere+ software...Read more

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Bacterial typing research application notes, literature & publications

Application notes and literature

  Bacterial Typing Application Note
  Ion S5 Infectious Disease Application Note


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  

Ferrario, et al. A genome-based identification approach for members of the genus Bifidobacterium.FEMS Microbiol Ecol. 2015 Mar;91(3). pii: fiv009. doi: 10.1093/femsec/fiv009. Epub 2015 Jan 27.  

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).

View all Ion Torrent  publications ›

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.