Rapid & Accurate de novo Microbial Sequencing


de novo sequencing in under a day powered by the Ion PGM System now with 400 base pair sequencing for long, accurate reads.




Application Notes & Publications

Read application notes and peer-reviewed publications to learn how the Ion PGM™ System has empowered advances in de novo sequencing.

Data Set

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

Informatics Solutions

Learn about small genome sequencing informatics solutions for the fastest way to get to your biological results.

Whole genome shotgun sequencing offers important new opportunities for the discovery and characterization of microbial organisms. For researchers characterizing the genomic structures of microbes, de novo sequencing and assembly of complete genomes is an important step. These basic research projects require deep coverage across the genome and high quality data. Ion Torrent™ Semiconductor sequencing has revolutionized de novo sequencing for microbial research. By democratizing sequencing through providing a simple, low cost system that delivers accurate results in less than a day, more and more sequencing projects that were previously unattainable due to budget or time constraints are now feasible. With 400 base pair sequencing on the Ion PGM™ System, sequencing assembly metrics are better than ever giving you a fast path to whole genome sequencing.

de novo Microbial Sequencing Workflow for the Ion PGM™ 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

The Ion PGM™ Sequencer enables rapid de novo sequencing with 400 or 200 bp sequencing. Runs are completed in just 3.7 hours...Read more

4 Analyze

Primary data analysis is performed using Torrent Suite Software. The DNAStar® SeqMan NGen® software package...Read more

de novo Microbial Sequencing Application Notes, Literature & Publications

Application Notes and Literature

Microbial Solutions Brochure
Discover how German scientists leveraged the Ion PGM™ Sequencer to get answers when faced with a serious public health outbreak (shiga toxin-producing E. coli outbreak in northern Germany)
The Ion PGM™ System, with 400-base read length chemistry, enables routine high-quality de novo assembly of small genomes


The Ion PGM™ System is cited in more than 40 peer-reviewed publications about small genome sequencing, making it the leading system for de novo assembly of small genomes.

Petrof, E., et al. (2013). Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut Microbiome 2013, 1:3. DOI: 10.1186/2049-2618-1-3

Hassan, S. S., et al. (2012). Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by rapid next generation sequencing technology Stand Genomic Sci 7(2): 189-199. DOI: 10.4056/sigs.3066455

Antwerpen, M., et al. (2012). Draft genome sequence of Bacillus anthracis BF-1, isolated from Bavarian cattle J Bacteriol 194(22): 6360-6361. DOI: 10.1128/JB.01676-12

Yergeau, E., et al. (2012). Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities Appl Environ Microbiol 78(21): 7626-7637. DOI: 10.1128/AEM.02036-12

View additional publications

Microbial Sequencing videos


de novo Microbial Sequencing 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.

de novo sequencing assembly specify workflows in third party software packages such as the DNAStar® - SeqMan NGen® software package automate genome assembly & closure. The DNAStar® - SeqMan NGen® software package offers both rapid reference-guided and de novo genome assembly while minimizing data analysis time (<2 hours with 10.5 GM of RAM).


Learn more about how this software can simplify your data analysis.

*Mellmann A, Harmsen D, Cummings CA et al. (2011) Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6, e22751; Rohde H, Qin J, Cui Y et al. (2011) Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 365, 718-724; Sherry NL, Porter JL, Seemann T et al. (2013) Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol. 2013 Feb 13. [Epub ahead of print ]

†The content provided herein may relate to products that have not been officially released and is subject to change without notice.
Ion Chef™ System is expected to be available for quotation and purchase in Q1 2013 and is expected to begin shipping in the first half of 2013.

For Research Use Only. Not for use in diagnostic procedures.