Ion TrueMate
Library Kits

Close the gap in de novo sequencing
with Ion TrueMate Library Kits
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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.


Ion 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 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 simple, low-cost 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 PGM System, sequencing assembly metrics are better than ever, giving you a fast path to whole-genome sequencing.

Mate-pair sequencing

For de novo genome assembly, a mate-pair approach enables large inserts from genomic libraries to be accommodated. Mate-pair sequencing approaches work by using a pair of tags with a given insert space that accommodates long inserts of several kilobases in length. One of the challenges with traditional mate-pair sequencing is that a relatively high number of chimeric molecules can form during the circularization/ligation steps, resulting in pairs of reads from different regions of the genome, creating what is called a “false mate”. These “false mates” mean that as many as 50% (or more) of sequence reads are wasted due to the insert being a concatemer instead of a single fragment.

The Ion TrueMate Library Kit generates mate-pair libraries with an insert size of 2–8 kb and uses “ChimeraCode™” and “Junction Code™” technology* to help ensure that the correct ends of the insert are sequenced (Table 1).

  Ion TrueMate Library Kit Competitor Kit A Competitor Kit B
Library size supported User-defined, 2-8 kb Ranges from 2-12 kb, with 2-5 kb more frequently observed 2-15 kb, difficult to control size
Chimeras Largely prevented, most chimeras detected Numerous chimeras, no chimera detection Numerous chimeras, no chimera detection
Mate pair efficiency >90% ~5% ~5%

How the Ion TrueMate Library Kit works

A mate-pair library is a specific type of DNA fragment library derived from fragments separated by several kilobases of intervening sequence. The resulting single end sequencing read consists of two juxtaposed sequence tags (a pair), each from opposite ends of the same long user-defined DNA fragment. The distance between reads on the original fragment is much longer than standard paired-end sequencing protocols, which makes it ideal for applications such as de novo genome sequencing, gap closure and genome finishing, repetitive genomes, and detection of structural variation.

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De Novo Microbial Sequencing Workflow for the Ion S5 System

1 Construct

The Ion TrueMate Plus Library Kit generates user-defined mate-pair insert libraries, and the Ion Xpress™ Plus Fragment Library Kit...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 S5 System enables high quality, rapid de novo sequencing with 400 or 200 bp sequencing.

4 Analyze

Primary data analysis is performed using Torrent Suite™ Software. DNASTAR™ Lasergene™ Genomics Suite provides an easy....Read more

De Novo Microbial Sequencing Application Notes, Literature & Publications

Application Notes and Literature

Ion S5 System infectious disease application note
Significantly improved de novo assembly of small genomes using the Ion TrueMate™ Plus Library Kit on the Ion PGM™ System
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 450 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

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 ›

On Top of Outbreaks

Hear Dag Harmsen, M.D. from the University of Münster discuss how the Ion PGM™ System provides fast and accurate whole-genome “shotgun” sequencing of microbes for disease research on retrospective samples from outbreaks.

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.

Ion PGM™ Hi-Q™ Sequencing Kit
Ion 16S™ Metagenomics Solution

*Lucigen is the registered trademark owner of ChimeraCode and JunctionCode; no ownership or sponsorship is implied herein.

†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 ]