Throughput flexibility of the Ion S5 Systems

The Ion GeneStudio S5 Series next-generation sequencing (NGS) instruments support five different sequencing chip types that scale to various levels of sample throughput, enabling a wide range of research applications. Select from various Ion chips to sequence a throughput range from 2M to 130M. Simply choose the chip type and instrument that matches your throughput and application needs.

This throughput flexibility enables cost-effective analysis of one to hundreds of samples and reduces the need to batch samples, helping make your workflow more efficient and your time to results faster. Different chip types can be combined in a single Ion Chef run when using Ion 510 & Ion 520 & Ion 530 Kit-Chef  and Torrent Suite Software version 5.6, allowing more flexibility not only in the throughput, but also in the workflow.

View and order Chip and Kit Products for the Ion S5 System ›

New: Ion 550 Chip for the Ion GeneStudio S5 Plus and Prime Systems

The new Ion 550 Chip generates 100–130 million sequencing reads on the Ion GeneStudio S5 Plus and Prime Systems using the automated workflow of the Ion Chef System. This chip is the fifth addition to our sequencing chip series, allowing scalability with a single instrument for clinical research applications. The Ion 550 Chip is not compatible with Ion GeneStudio S5 System. 

The Ion 550 Chip offers: 

  • Greater throughput of the Ion GeneStudio S5 Plus and Prime Systems—a good choice for exome and transcriptome sequencing, liquid biopsy, or large oncology panels
  • Flexible Ion 550 Chef workflow—1 or 2 loaded chips per Ion Chef run, with no loss of reagents

Learn more about Ion GeneStudio S5 Series

  Ion GeneStudio S5 series specifications ›

What our users say about throughput flexibility
“I need to be able to vary the number 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 the smaller-throughput chip.” 

— Dr. Jean Francois Laes, Chief Technology Office, OncoDNA, Belgium

“[The Ion Torrent NGS System] is so flexible with different chip types and outputs. You can use it for small sequencing projects up to quite large projects so you really have the flexibility that was not possible with previous systems.”  

— Inger Jonasson, Laboratory Manager, Uppsala University Genome Center, Sweden


Choosing the right chip type for your throughput/application

Example of our popular panels and applications Panel description Number of samples per run*
Ion 510 Chip
2-3M reads
Ion 520 Chip
4-6M reads
Ion 530 Chip
15-20M reads
Ion 540 Chip
60-80M reads
Ion 550 Chip
100-130M reads
Cancer research
Ion AmpliSeq Cancer Hotspot Panel v2 Identify cancer hotspot SNVs from 10 ng of FFPE derived DNA 4 8 26 84 NA
Oncomine Focus Assay  Identify solid tumor-relevant SNVs, indels, CNVs, and gene fusions from 52 genes 4 8 26 NA NA
Oncomine Comprehensive Assay v3 Enable biomarker discovery of SNVs and indels and full gene sequencing from 161 genes NA NA NA 8 16
Oncomine Lung cfDNA Assay Detect rare somatic mutations in genes relevant to non-small cell lung cancer NA NA 8 32 ~60-64
Oncomine Pan-Cancer Cell-Free Assay Detect rare somatic mutations in genes across multiple cancer types NA NA 1 4 7-8
Oncomine Immune Response Research Assay interrogate genes  involved in immune response pathways NA 4 8 NA NA
Gene expression
Ion AmpliSeq Transcriptome Human Gene Expression Kit Research global gene expression levels NA NA 2 8 16
Ion AmpliSeq Transcriptome Mouse  Gene Expression Kit Research global gene expression levels NA NA 2 8 16
Inherited disease research
Ion AmpliSeq Exome RDY Panel  Discover rare mutations of the whole exome NA NA NA 2 4
Ion AmpliSeq Pharmacogenomics Research Panel (40 genes) Investigate known variants associated with drug metabolism 48 96 384 384 NA
Ion AmpliSeq On-Demand Panel  Identify variants in genes associated with inherited disease Up to 384 (varies by number of genes in panel)
Reproductive health
Ion ReproSeq PGS on Ion S5 System Detect aneupoloidy using DNA from preimplantation embryos 16 24 96 NA NA
Infectious disease research
Ion AmpliSeq
TB Research Panel
Identify variants associated with antimicrobial resistance in Mycobacterium tuberculosis (TB) 48 84 272 384 NA
Ion AmpliSeq Ebola Research Panel Identify the presence of Ebola virus 48 84 272 384 NA
Ion 16S Metagenomics Kit Identify bacterial species in mixed samples  24 48 192 NA NA
* The number of samples per run/chip serves as a guide, and the actual number of samples loaded will depend on your needs for number of reads and depth of coverage. It is important to note that as the number of libraries per chip increases, it becomes more difficult to balance the reads between libraries. In addition, libraries from FFPE tissue tend to produce more variable results. We suggest combining fewer libraries initially and determining real limits empirically.
Cancer Genomics Transcriptomics Research

Cancer genomics and transcriptomics research

Low Frequency Mutations Cell Free DNA

Low-frequency mutations from cell-free DNA

Reproductive Genomics Inherited Disease Research

Reproductive genomics and inherited disease research

Rapid Sequencing Microorganisms

Rapid sequencing of microorganisms

Watch more demos of Ion GeneStudio S5 workflow

Learn more about Ion GeneStudio S5 applications