De Novo Microbial Sequencing

Rapid de novo sequencing of microbes

Get your results in as little as 24 hours on the Ion S5 System

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Infectious disease research app note

Application Notes & Publications

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

Data Set

Download a data set generated on the Ion GeneStudio S5 System and see the results for yourself.

Ion GeneStudio S5 System

Adopting next-generation sequencing (NGS) in your lab is now simpler than ever before with industry-leading speed and affordability, with the flexibility to do multiple sequencing applications on a single system.

Whole-genome sequencing offers important new opportunities for the discovery and characterization of viral, bacterial, and fungal organisms. For researchers characterizing the genomic structures of microbes, de novo sequencing and assembly of 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 a fast, simple, affordable system that is designed to deliver 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 S5 System, and the Ion PGM™ System with Ion Hi-Q™ chemistry, sequencing assembly metrics are better than ever, with up to a 90% decrease in indel error rates for microbial sequencing (Figure 1), giving you a fast path to whole-genome sequencing.

Figure 1. Decrease in indel false positives for microbial de novo assembly, using the Ion PGM™ Hi-Q™ Sequencing Kit instead of the Ion PGM™ Sequencing 200 Kit v2. Template preparation for 200-base read fragment libraries was performed using the Ion PGM™ Template OT2 200 Kit. Indel error rate per 100 kb analysis performed with SPAdes 3.1 delta-score filter.

Construct de novo libraries

Ion Xpress™ Plus Fragment Library Kit

The Ion Xpress Plus Fragment Library Kit provides rapid and flexible enzyme-based library construction in as little as 2 hours for gDNA and amplicon libraries, with significantly higher yields and lower bias than other library construction techniques.

Thermo Scientific MuSeek Library Preparation Kit

The MuSeek™ Library Preparation Kit provides a fast and simple transposon-based method for preparing high-quality genomic DNA libraries for Ion Torrent sequencing. The kit utilizes MuA transposase for fragmentation and simultaneous tagging of the target DNA, enabling library construction in as little as 80 minutes.

De novo microbial sequencing workflow for the Ion S5 System


Your choice of fragment library preparation kits, enables low-cost sample preparation for de novo sequencing of microbial genomes.
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The Ion Chef™ System provides simple, high-throughput template preparation with only minutes of hands-on time.
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The Ion GeneStudio S5 System enables high quality, rapid de novo sequencing with 400 or 200 bp sequencing.


Primary data analysis is performed using Torrent Suite™ Software. DNASTAR™ Lasergene™ Genomics Suite provides an easy-to-use interface for genome assembly.

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.

By expanding the functionality of the current on-board software, plugins offer a powerful means to manage a full range of additional applications and analyses. Torrent Suite Software allows you to customize your analysis at the end of each run through the use of different plugins—de novo assembly, resequencing, and metagenomics applications are included in the software—which are available for download in the Torrent Browser Plugin Store.

DNASTAR - Ion Torrent: De Novo Bacterial Genome

DNASTAR - SeqMan NGen software enables you to assemble reads from any major next-gen sequencing platform, including Ion Torrent platforms, with just a few simple steps.

This video demonstrates a de novo bacterial genome assembly of Ion Torrent data and post-assembly analysis, including annotating the consensus via a BLAST search and reviewing the depth of coverage.


Application notes and literature

Ion GeneStudio S5 System infectious disease application note
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
Ion Hi-Q™ chemistry for the Ion PGM™ System


The Ion PGM System is cited in more than 500 peer-reviewed publications about small-genome sequencing, making it the leading system for de novo assembly of small genomes.

Veras AAO, Sá PHCG, Pinheiro KC, Graças DA, Baraúna RA, et al. (2014). Efficiency of Corynebacterium pseudotuberculosis 31 Genome Assembly with the Hi-Q Enzyme on an Ion Torrent PGM Sequencing Platform. J Proteomices Bioinform 7: 374-378. DOI: 10.4172/jpb.1000342

Soni I, Chakrapani H, Chopra S. (2015). Draft Genome Sequence of Methicillin-SensitiveStaphylococcus aureus ATCC 29213 Genome Announc 3(5): e01095-15. DOI: 10.1128/genomeA.01095-15

Holmes A, Allison L, Ward M, Dallman TJ, Clark R, Fawkes A, Murphy L, Hanson M (2015). Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance J Clin Microbiology 53: 3565-3573. DOI: 10.1128/JCM.01066-15

Orsini M, Mangone I, DiPasquale A, Perticara S, Sacchini L, Cito F, Iannetti S, Marcacci M, Ancora M, Calistri P, Di Giannatale E, Cammà C (2015). Draft Genome Sequences of 19 Salmonella enterica Serovar Typhimurium [4,5:i:] Strains Resistant to Nalidixic Acid from a Long-Term Outbreak in Italy Genome Announc 3(4):e00911-15. DOI: 10.1128/ genomeA.00911-15

Da Silva Sanotos AC, Rodrigues J. (2015). Draft Genome Sequence of Shiga Toxin-ProducingEscherichia coli Strain D92/09 Genome Announc 3(4): e00805-15. doi:10.1128/genomeA.00805-15

Mattos-Guaraldi AL, Guimarães LC, Santos CS, Veras AAO, Carneiro AR, Soares SC, Ramos JN, Souza C, Vieira VV, Hirata R, Jr, Azevedo V, Pacheco LGC, Silva A, Ramos RTJ (2015). Draft Genome Sequence of Corynebacterium striatum1961 BR-RJ/09, a Multidrug-Susceptible Strain Isolated from the Urine of a Hospitalized 37-Year-Old Female Patient Genome Announc 3(4):e00869-15. DOI: 10.1128/genomeA.00869-15

Small-genome sequencing

Learn about how Ion Torrent sequencing has enabled customers in their microbiology research.

†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 ]





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