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Fast and affordable sequencing for outbreak investigation research

 Ion Torrent systems provide the ultra-high sensitivity, scalability, and rapid turnaround time vital to outbreak investigation research.

Request a quote     Ion S5 Infectious Disease application note

Bacterial typing workflow for the Ion GeneStudio S5 System
Construct library

The Ion Plus Fragment Library Kit or Ion Xpress Plus Fragment Library kit provides low-cost sample preparation in as little as two hours for gDNA and amplicon libraries.

Prepare template
  • The Ion Chef Instrument provides simple, fully automated high-throughput templating preparation with only minutes of hands-on time
  • The OneTouch 2 System is an alternative, semi-automated template preparation solution for up to 600 bp sequencing runs
Run sequence

The Ion GeneStudio 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.

analyze data

Primary data analysis is performed using Torrent Suite Software. The Ridom SeqSphere+ software package provides a follow-on solution for bacterial typing.

Construct library

The Ion Plus Fragment Library Kit or Ion Xpress Plus Fragment Library kit provides low-cost sample preparation in as little as two hours for gDNA and amplicon libraries.

Prepare template
  • The Ion Chef Instrument provides simple, fully automated high-throughput templating preparation with only minutes of hands-on time
  • The OneTouch 2 System is an alternative, semi-automated template preparation solution for up to 600 bp sequencing runs
Run sequence

The Ion GeneStudio 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.

analyze data

Primary data analysis is performed using Torrent Suite Software. The Ridom SeqSphere+ software package provides a follow-on solution for bacterial typing.


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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 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.

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Application notes and literature

Bacterial typing research application notes, literature & publications

  Bacterial Typing Application Note
  Ion S5 Infectious Disease Application Note

Publications

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.

Rapid High Resolution Genotyping of Francisella tularensis by Whole Genome Sequence Comparison of Annotated Genes (“MLST+”).   Antwerpen MH (2015) PLoS ONE 10(4): e0123298. doi:10.1371/journal.pone.0123298

A genome-based identification approach for members of the genus Bifidobacterium.  Ferrario et al. 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.  Vogel et al. (2012) J Clin Microbiol JCM.00038-12 [pii];10.1128/JCM.00038-12 [doi]. 

Multilocus sequence typing of total-genome-sequenced bacteria.  Larsen et al. (2012). J Clin Microbiol. JCM.06094-11 [pii];10.1128/JCM.06094-11 [doi]. 

View all Ion Torrent  publications ›