The 5500xl Genetic Analyzer, Catalog # 4460730 has been discontinued. The Ion Torrent S5 Sequencers are available as alternatives to this product. View discontinuation letter ›

5500xl Genetic Analyzer

Catalog number: 4460730

Applied Biosystems™  Related applications: Chromatin Biology | DNA Sequencing | Epigenetic Sequencing | Methylation Analysis | RNA Sequencing | SOLiD® Next-Generation Sequencing

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Never before has a next-generation sequencing platform provided the combination of accuracy, sensitivity, and cost effectiveness to support your large translational research studies–until now. The new 5500xl Genetic Analyzer (Figure 1) helps ensure optimal productivity with two flexible FlowChips, embedded quality controls, intuitive user workflows, and project scalability. With the 5500xl Genetic Analyzer, you are empowered to discover rare genetic events or sub-populations of somatic mutations at an unprecedented pace.

Key Benefits
• Sequencing right here, right now
• Cost-effective sequencing runs with individually configurable lanes
• Superior low frequency variant detection for whole exome sequencing or targeted resequencing
• Reproducibility, reliability, and quality for your RNA applications
• Confidence and uniformity in multiplexing with up to 96 barcodes
• Optimal analysis solutions for streamlined productivity and freedom to operate

When Coverage is Not Enough
Additional sequence coverage fails to compensate for poor accuracy in the detection of rare variants that may hold the key to a better understanding cancer progression, disease penetrance, or drug resistance. With a system accuracy of up to 99.99%, the 5500xl Genetic Analyzer enables you to perform 25% less sequencing to detect rare variants than a next-generation sequencing platform with 99.99% system accuracy in order to detect somatic variant present at 1% (Figure 2). The industry-leading accuracy of the 5500xl Genetic Analyzer enables detection of significant biological variation for applications like whole genome resequencing, targeted resequencing, and whole transcriptome analysis.

When Flexibility, Speed, and Cost are Crucial
Multidisciplinary translational research programs often require processing of multiple samples across multiple applications like whole exome, RNA-seq, and structural variation. The 5500xl Genetic Analyzer provides you the flexibility to configure your sequencing runs to your project and throughput needs (Figure 3). The system’s two configurable microfluidic FlowChips process up to 12 independent samples and the intelligent barcoding kits multiplex up to hundreds of samples in a single run. Pay-Per-Lane Sequencing (PPL-Seq™) and independent run lanes tailor the system to any project scale. With the 5500xl Genetic Analyzer, avoid project delays by optimizing your run configurations to attain the lowest cost per sample.

When the Utmost Productivity and Efficiency are Essential
Ease of use, quality control, and speed are integral components of any next-generation sequencing workflow. Co-developed with Hitachi-Hi Technologies, the 5500xl Genetic Analyzer's elegant tabletop design (Figure 1) is built off “Six-Sigma" processes to streamline your research. The 5500xl Genetic Analyzer delivers streamlined fluidics and a simple, intuitive graphical user interface (GUI) for easy setup and run monitoring. Real-time analysis and 60% smaller data footprints expedite data export and analysis time. Additionally, with embedded sequencing controls and reagent usage tracking, the 5500xl Genetic Analyzer empowers you to obtain extremely high-quality and biologically meaningful data out of every sequencing run.

Take Comprehensive Research to New Heights
The superior accuracy, flexibility, and productivity of the 5500xl Genetic Analyzer accelerate comprehensive research. Larger translational medicine initiatives, genome consortiums, and disease-subtype stratification projects with resulting groundbreaking publications are now within your grasp. Catch them all with the new 5500xl Genetic Analyzer.

A Community of Support
With more than 2,000 field personnel, we have the most extensive network of dedicated Field Application Specialists and Service Engineers to work with you, so that you can feel confident that we will be there when and where you need us most.

The 5500xl Genetic Analyzer is For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.
For Research Use Only. Not for use in diagnostic procedures.


Run Time: 24 hrs
Dimensions: 120 mm x 750 mm x 800 mm
Throughput: Microbeads: Up to 20-30 Gb⁄day, Nanobeads: Up to 30-45 Gb⁄day
Data Output: .xsq files, .bam files
Read Length: 75 bp (fragment), Up to 60 bp x 60 bp (mate-paired), 75 bp x 35 bp (paired-end)
Library Type: Fragment Library, Mate-Paired Library, Paired-End Library
Product Size: 1 instrument
Voltage Limit: 240V
Number of Lanes: 12 lanes
System Accuracy: 0.9999
Sequencing Scale: genome, transcriptome, exome
Display Interface: GUI
External Computer: Tower Computer
Downstream Application: Next-Generation Sequencing
For Use With (Equipment): 5500xl Genetic Analyzer
High Throughput Compatibility: Multiplexing

Contents & storage

Located between sea level and 2000m (6500 ft.) above sea level

Sequencer, computer, and the UPS unit
20%–80% (noncondensing)

Note: The room temperature must not fluctuate more than 2°C over a 2-hour period.


Manuals & protocols