Ion S5 and Ion S5 XL Systems

Targeted sequencing has never

been simpler
Explore the Ion S5
and Ion S5 XL Systems
Adopting next-generation sequencing (NGS)
in your lab is now simpler than ever

The Ion S5™ and Ion S5™ XL Systems provide the simplest Ion S5 Systems
DNA-to-data workflow for targeted sequencing with • Ion S5 System—simple workflow,
industry-leading speed and affordability. This allows you to fast sequencing, lower weekly
spend less time doing repetitive lab work, and more time throughput
answering the critical questions in your research.
• Ion S5 XL System—simple workflow,
faster data analysis, higher weekly
Want to sequence small gene panels or
throughput
bacterial genomes on Monday, and exomes or
transcriptomes on Wednesday? Ion S5 and Ion S5 XL
Systems let you leverage a single benchtop instrument that
scales to your application and throughput needs.

Ion Torrent™ technology has been referenced in over 3,300

publications to date. Now you can drive your research
forward using this highly cited technology with the latest
innovation in leading-edge benchtop NGS: the Ion S5 and
Ion S5 XL Systems.

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 “That’s it? That’s all I have to do?
This is really easy to set up.”
Susana Häggqvist
Research Engineer
Uppsala Genome Center, Sweden

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The S is for

Simplicity
Ready. Set. Sequence.
The Ion S5 and Ion S5 XL Systems come with
load-and-go reagents and a straightforward user
interface, so you can set up the sequencer in less
than 15 minutes of hands-on time.

You can also track your consumables with ease

and accuracy with the automated radio frequency
identification (RFID) tracking feature of the systems.

By adding an Ion Chef™ System to your lab, you

can benefit from automated library and template
preparation, so you can go from DNA to data in less
than 45 minutes of total hands-on time.

Cartridge-based Ion Chef System Automated tracking

reagents 30 minutes of hands-on of consumables
Less than 15 minutes of time for library and Easy and accurate
sequencing setup time template prep RFID tracking

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The S is for

Scalability
Single sequencer. Multiple applications.
Focus your efforts on applications that have Cancer research
the potential to be impactful.

Each Ion S5 and Ion S5 XL System currently

supports four different chip types that scale to
various levels of sample throughput, enabling a
wide range of research applications. Select from
various Ion chips for a throughput range of 2 to Gene expression

80 million reads per run using just one instrument.

This flexibility also means reduced need for sample

batching to achieve optimum cost efficiency. Just
select the chip type that matches your specific Inherited disease research

throughput or application needs.

“I need to be able to vary the number Reproductive health

and type of samples I put onto a run in
any given week, but not compromise on
cost per sample. If we have a lower
number of samples we can run them on Infectious disease
the smaller throughput chips. The Ion S5 XL research

(System) offers this flexibility.”

Dr. Jean-François Laes
Chief Technology Officer
OncoDNA, Belgium

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 Choosing the right chip type for your
Number of samples per run
throughput and application
Example of our
popular panels and
applications Panel description Ion 510 Chip Ion 520 Chip Ion 530 Chip Ion 540 Chip
Ion AmpliSeq™ Cancer Identify cancer hotspot SNVs from
4 8 26 84
Hotspot Panel v2 10 ng of FFPE DNA
Identify solid tumor–relevant SNVs,
Ion Torrent™ Oncomine™ Focus indels, CNVs, and gene fusions
4 8 26 NA
Assay from 52 genes, with a single
workflow using FFPE samples
Enable biomarker discovery of
SNVs and indels and full gene
Ion Torrent Oncomine
™ ™

sequencing from 161 genes, NA NA NA 8

Comprehensive Assay v3
with a single workflow using
FFPE samples
Detect rare somatic mutations
Ion Torrent™ Oncomine™ Lung down to 0.1% in genes relevant to
NA NA 6 24
cfDNA Assay non-small cell lung cancer, using
one tube of blood
Ion Torrent™ Oncomine™ Interrogate genes involved in
Immune Response Research immune response pathways, with NA 4 8 NA
Assay a targeted gene expression assay

Analyze the whole transcriptome

Ion Total RNA-Seq Kit v2 with strand-specific RNA NA NA NA 2
sequencing

Ion AmpliSeq™ Transcriptome Research global gene expression

NA NA 2 8
Human Gene Expression Kit levels from 10 ng of FFPE RNA
Discover SNPs, indels, and CNVs
Ion AmpliSeq™ Exome RDY for research on rare or unknown
NA NA NA 2
Panel disorders, by whole-exome
sequencing
Ion AmpliSeq™
Investigate known variants
Pharmacogenomics 48 96 384 384
associated with drug metabolism
Research Panel (40 genes)*
Discover variants in the most
Ion AmpliSeq™ On-Demand
relevant genes in inherited disease Up to 384 (varies by number of genes in the panel)
Panel (up to 300 genes)
research

Detect aneupoloidy using DNA

Ion ReproSeq™ PGS on Ion from single or multiple cells
16 24 96 NA
S5™ System biopsied from preimplantation
embryos

Ion AmpliSeq™ TB Research Assess known variants associated

48 84 272 384
Panel with antibiotic resistance
Identify the presence of Ebola virus
Ion AmpliSeq™ Ebola
quickly, accurately, and cost- 48 84 272 384
Research Panel
effectively
Identify bacterial species in mixed
Ion 16S™ Metagenomics Kit 24 48 192 NA
samples

* Assuming 400x coverage.

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The S is for

Speed
Because every hour counts.
A few hours could make all the difference in
your quest for the right answer.
Sequencing run times
Unlike light-based sequencers, there are of 2.5–4 hours

no cumbersome optics or labeled nucleotides DNA to data in as little as

24 hours
with semiconductor sequencing technology.
The Ion S5 Systems are the only benchtop
NGS platforms with run times as short as
2.5 hours, and rapid DNA-to-data workflows
that can be completed in as little as 24 hours.

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The S is for

Small sample input

Because every sample matters.
Explore complex pathways with your low-input or
degraded samples with Ion AmpliSeq™ technology,
which enables you to prepare libraries from just a As little as 1 ng of
DNA or RNA
few nanograms of low-quality DNA or RNA. For low-quality,
low-input samples
Cited by hundreds of publications in just four years—
you can count on this highly referenced technology for
consistent and robust library preparation.

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The S is for

Simple data analysis

and storage
Go from data to variants in a few clicks.
Whether you are new to NGS or an
experienced user, Torrent Suite™ Software
and Ion Reporter™ Software make it easy
for you to get started with NGS.

Primary analysis:
Torrent Suite Software
• Easily plan, monitor, track, and
analyze your runs using the web-
based interface

• Conduct raw data analysis,

alignment, and variant calling with
optimized plug-ins

Secondary analysis:
Ion Reporter Software
• Integrate, annotate,
and interpret variants

• Cloud or on-site options available to

meet your needs

Data storage
• Securely store and retrieve
sequencing runs and data using
Torrent Storage™ NAS Devices and/
or Ion Torrent™ DataSafe™ Solutions

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The S is for

Ion S5 Systems

Simple, scalable, and rapid workflow for panels, microbes, exomes, and transcriptomes

Ion S5 System Ion S5 XL System

Ion 510 Ion 520 Ion 530 Ion 540 Ion 510 Ion 520 Ion 530 Ion 540
Chip† Chip Chip Chip Chip† Chip Chip Chip
15–20 60–80 15–20 60–80
Reads 2–3 million 4–6 million 2–3 million 4–6 million
million million million million

200 bp 0.3–0.5 Gb 0.6–1 Gb 3–4 Gb 10–15 Gb 0.3–0.5 Gb 0.6–1 Gb 3–4 Gb 10–15 Gb

Output*
400 bp 0.6–1 Gb 1.2–2 Gb 6-8 Gb — 0.6–1 Gb 1.2–2 Gb 6-8 Gb —

200 bp 2.5 hr 2.5 hr 2.5 hr 2.5 hr 2.5 hr 2.5 hr 2.5 hr 2.5 hr

Run time
400 bp 4 hr 4 hr 4 hr — 4 hr 4 hr 4 hr —

200 bp 2 hr 5 hr 8 hr 16.5 hr 0.5 hr 1 hr 2.5 hr 5 hr

Analysis
time**
400 bp 6.5 hr 8 hr 17.5 hr — 0.5 hr 2 hr 4 hr —

Long-read sequencing for research applications such as human leukocyte antigen (HLA) typing or
metagenomic analysis

Ion S5 System Ion S5 XL System

Ion 510 Ion 520 Ion 530 Ion 540 Ion 510 Ion 520 Ion 530 Ion 540
Chip†† Chip Chip Chip†† Chip†† Chip Chip Chip††
9–12 9–12
Reads — 3–4 million — — 3–4 million —
million million

Output* 600 bp — 0.5–1.5 Gb 1.5–4.5 Gb — — 0.5–1.5 Gb 1.5–4.5 Gb —

Run time 600 bp — 4 hr 4 hr — — 4 hr 4 hr —

Analysis
600 bp — 8 hr 17 hr — — 2.5 hr 4.5 hr —
time**
* Expected output with >99% aligned or measured accuracy. Output dependent on read length and application.
** Analysis time to aligned BAM files.
† Ion 510 Chip is only compatible with the Ion Chef System workflow for template preparation. The Ion 510 Chip is not enabled for the Ion OneTouch™ 2 System template preparation workflow.
†† 600 bp sequencing is not enabled for Ion 510 Chip and Ion 540 Chip.

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Service and support

We are here to help.

With more than 3,700 global sales, service, We invite you to start sequencing with the Ion S5 and
and technical support specialists available to Ion S5 XL Systems, based on technology adopted by your
assist you in person, by phone, or online, you peers and supported by our scientists.
can be confident that we will be there when
and where you need us most.

Europe
60 field application specialists,
103 field service engineers

Americas
90 field application specialists,
120 field service engineers

Asia Pacific
22 field application specialists,
33 field service engineers

Start your sequencing journey at thermofisher.com/ions5

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