The 5500 Genetic Analyzer, Catalog # 4452865 has been discontinued. The Ion Torrent S5 Sequencers are available as alternatives to this product. View discontinuation letter ›
Applied Biosystems™

5500 Genetic Analyzer

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Built on three decades of sequencing expertise and powered by the proven accuracy of ligation-based sequencing, the new 5500 Genetic Analyzer provides a robust, affordable next-generation sequencing platform for every lab. Designed to give you the choice to optimize for turnaround time or throughput, the 5500 Genetic Analyzer is a highly accurate, cost-effective solution for analyzing one or many samples.

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

Explore the Depths of Translational Research
With Exact Call Chemistry, the industry-leading accuracy of the 5500 Genetic Analyzer helps you get definitive answers about biological variation for applications like whole exome, RNA-seq, and structural variation.

Customize the System for Your Projects
The 5500 Genetic Analyzer allows you to tailor your sequencing runs precisely for your research. The six independent FlowChip lanes and Pay-Per-Lane Sequencing (PPL-Seq™) allow you to configure the instrument to different project scales and application types. Additionally, the system’s intelligent barcode kits can accommodate from one to hundreds of samples in a single run.

Don’t Wait
With the 5500 Genetic Analyzer, the unique capability to run each FlowChip lane independently allows you to turn around results in the shortest time possible. Now you can explore the genome, transcriptome, and epigenome with a hypothesis-neutral platform that combines powerful sequence data generation with premium accuracy. Whether you're running whole exome, RNA-seq, or a structural variation experiment, the 5500 Genetic Analyzer is designed to deliver high-quality results in a time-sensitive and cost-effective manner.

Perform Sequencing with Ease
Designed in collaboration with core facilities and principal investigators, the integrated 5500 Genetic Analyzer provides an intuitive and user-friendly workflow from sample preparation to data analysis.

Workflow Benefits Include:
• Embedded sequencing controls to enable real-time monitoring of data quality throughout the entire workflow
• System alerts to help maximize data quality and system performance, and to track reagent usage during the course of the sequencing run
• Easy-to-use software, 60% smaller data footprints, workstation computing, and standard base sequence file formats to facilitate setup, daily operations, and seamless integration with data analysis tools

Join the Era of Genomic Medicine
The throughput, broad range of applications, system flexibility, and intuitive design of the 5500 Genetic Analyzer address the needs of core and services laboratories, and basic and clinical research labs, to take sequencing into every scientific discipline.

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 in the industry. You can feel confident that we will be there when and where you need us most.

The 5500 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.


Data Output: .bam files, .xsq files
Dimensions: 120 mm x 750 mm x 800 mm
Display Interface: GUI
Downstream Application: Next-Generation Sequencing
External Computer: Tower Computer
For Use With (Equipment): 5500 Genetic Analyzer
High Throughput Compatibility: Multiplexing
Library Type: Fragment Library, Mate-Paired Library, Paired-End Library
Number of Lanes: 6 lanes
Product Line: SOLiD™
Product Size: 1 instrument
Read Length: 75 bp (fragment), 75 bp x 35 bp (paired-end), Up to 60 bp x 60 bp (mate-paired)
Run Time: 24 hrs
Sequencing Scale: exome, genome, transcriptome
System Accuracy: 0.9999
Throughput: Up to 10-15 Gb per day
Voltage Limit: 240V

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