Fragment Analyzer

Introducing one powerful instrument to cover the full spectrum of DNA, gDNA and RNA quality control. The Fragment Analyzer does everything from high-resolution analysis to fast DNA separations, across the widest separation range.

AATI Scientist looking at data

What is the Fragment Analyzer?

The Fragment Analyzer is a parallel capillary electrophoresis instrument designed to eliminate laboratory bottlenecks caused by slow and unreliable QC analysis of nucleic acids. These bottlenecks are resolved by the automation of key steps such as gel loading and sample injection. After separations are complete, nucleic acid fragment analysis is simplified with ProSize Data Analysis Software. Together, the Fragment Analyzer and ProSize offer researchers the ability to quickly and reliably QC their samples and move on to downstream applications sooner.

High Separation Resolution
Resolve a wide range of DNA and RNA fragments. Achieve as low as 3 bp resolution with high sizing accuracy.
Low Cost per Sample
Choose Qualitative or Quantitative gel kits that best suit your analysis needs. Realize lower operational costs than other analytical instruments.
Decreased Prep Time
With room temperature stable reagents and no daily array handling, minimal work is needed to setup runs.
View Data in Real-Time
See results as they are generated and change electrophoresis times during a run if desired.
Wide Dynamic Range
Most gel kits cover approximately two orders of magnitude. High and Standard Sensitivity Kits are available for most applications, extending the overall range of detection.
User-Friendly Software
Automate data scoring. Calculate fragment size and concentration. Create, save and load customized reports and scoring parameters for flagging and smear analysis.

How flexible is the Fragment Analyzer?

It [The Fragment Analyzer] is working wonderfully! Very well built and incredible device.

Jeremy Prokop, Michigan State University
Grand Rapids Research Center.

Versatility defines the Fragment Analyzer. Not only are researchers able to perform DNA analysis and RNA analysis using the same capillary array, they can easily modulate throughput with the option of array cartridges with 12, 48 or 96 capillaries in varying lengths. Users can run a few samples up to 288 samples without intervention, making the instrument perfect for laboratories that analyze a dozen RNA samples per week, to high-throughput genomic facilities that analyze nucleic acid samples by the thousands.

Flexible enough to handle any workflow senarios

The Fragment Analyzer is able to QC a wide range of nucleic acids saving you time and improving workflow efficiency.
Select the 5200 Fragment Analyzer with a 12 capillary array, or the 5300 Fragment Analyzer with a 48 or 96 capillary array, all in variable lengths, to suit your labs throughput needs. Change arrays as needed to match the changing needs of your lab.
Load up to three trays of 96-well plates at a time, allowing you to run up to 288 samples without human intervention.
Set up two gels at one time, which allows you to program distinct separation methods that require the use of different separation gels or large runs of a single application for completely automated operation.

ProSize Data Analysis Software

The flexibility of the Fragment Analyzer platform extends to post-electrophoresis processing with ProSize, powerful yet intuitive software that automatically performs fragment analysis. ProSize provides a core set of measurements for every sample: fragment/smear size and concentration while simultaneously enabling users to confirm quality with an electropherogram and digital gel image. Notably, specialized, sample dependent metrics are available including: GQN, RQN, DQN, DV200, the evaluation of CRISPR induced mutations, Smear Analysis, and quantification of microRNA present in sample.


A quality metric developed by Illumina
for ProSize. Provides unmatched assessment of FFPE RNA quality prior to sequencing through analysis of formalin-fixed, paraffin-embedded (FFPE) RNA
tissue before running in TrueSeq.
Learn more
Quickly quantify and
qualify DNA and RNA samples
with ProSize Data Analysis
Software. Data is automatically processed and an electropherogram, digital gel image, and a summary of nucleic acid size and concentration
are provided. Further analysis tools
are available to meet unique
user demands.


Eliminate unnecessary sequencing
from CRISPR workflows. When used in conjunction with the CRISPR family of kits from Agilent, the CRISPR
Plugin identifies positive clones,
providing % Cleaved, % Mutation,
and zygosity.


The Fragment Analyzer – with variable throughput, a single array for DNA and RNA, and the power of capillary electrophoresis – is a versatile instrument ideal for all applications. Agilent - formerly Advanced Analytical (AATI) manufactures reagent kits covering the full range of nucleic acid analysis applications, from NGS library validation to genotyping. Common RNA and DNA analysis applications are listed below.


CRISPR gene editing has swept the life sciences by storm. Use the power of CE to streamline CRISPR workflows with reliable reagent QC and a simple and accurate screening process while simultaneously elucidating the zygosity of positive clones.

> Learn more...


NGS library QC is essential to the generation of successful sequencing results. Several solutions have been developed to deal with the QC challenges of various types of NGS libraries, from short-read to long-read sequencing platforms, ChIP-seq, RNA-seq, and beyond.

> Learn more...

Genomic DNA

An accurate understanding of genomic DNA quality, quantity, and size is important for numerous methodologies including evaluating isolation success and NGS. Methods of evaluating the quantity, quality, and size of gDNA exist, though many are unable to reliably resolve challenges associated with genomic DNA analysis.

> Learn more...

PCR Fragments

Determination of amplicon size and concentration is a crucial aspect in post-reaction analysis of PCR. Traditional methods of PCR fragment analysis lack the sensitivity and resolution demanded by many applications.

> Learn more...


Active in myriad biological processes, RNA is the target of many applications, from microarrays to NGS. With diverse types of RNA, small RNA, mRNA, rRNA, and more, unique analytic challenges are posed. Several solutions for the quantification, qualification, and sizing of RNA samples have been developed, though many do not fully address the analytic challenges.

> Learn more...


Cell-free DNA (cfDNA) is of increasing interest to clinicians and researchers alike as a promising biomarker for various disease states. cfDNA requires rigorous assessment of quality prior to use in NGS workflows to ensure successful sequencing results.

> Learn more...

Large Fragment DNA

The advent of next-generation long read sequencing and synthetic genomics has increased interest in large DNA fragment analysis. Ideal for QC steps in the SMRTBell library workflow from Pacific Biosciences®, the large fragment DNA kits for the Fragment Analyzer can quantify and qualify DNA fragments and smears through 50 Kb.


Commonly employed in plant genetics, TILLiNG (Targeting Induced Local Lesions in Genomes) is a reverse genetics approach used to discover small and point mutations, such as SNPs. Detection of TILLiNG induced mutations depend on heteroduplex assays.

> Learn more...

Plasmid DNA

Assessment of the amount of supercoiled plasmid DNA in a sample is a critical measurement for many applications, such as: purifications, DNA vaccines, and gene therapy products. The Plasmid DNA Analysis Kit (DNF-940) delivers high quality sizing and relative quantification of supercoiled plasmid.

Commonly analyzed nucleic acid samples include:

  • NGS Libraries (Illumina and PacBio)
  • Plasmid (supercoild and linear)
  • SSR/Microsatellites
  • PCR Amplicons

Technical Information


Parallel capillary electrophoresis (CE) paired with fluorescent detection enables analytical separations of DNA and RNA. Central to CE is the capillary array. The Fragment Analyzer has several array configurations available with 96 capillaries, 48 capillaries, or 12 capillaries in an 8 x 12 format, a 4 x 12 format, or a 1 x 12 format, respectively. Electrodes adjacent to each capillary facilitate the direct electrokinetic injection of sample into the capillaries from a standard 96-well plate. Capillaries are arranged in parallel when passing through the detection window, positioned between the LED and the CCD detector assembly.

Diagram Parallel Capillary Electrophoresis Array

Nucleic acid detection is accomplished with a rigorously designed optical platform comprised of an LED light source (470 nm excitation), camera lens, and CCD detector. Fluorescent light passes from the LED through the array window. The emitted fluorescence from the intercalating dye then passes through the camera lens and specific band pass filters and spatially imaged onto the CCD detector. This system enables real-time detection of nucleic acid separations.

The power supply provides appropriate voltage for electrokinetic sample injection and electrophoresis. Recommended operating limits are +/-16 kV, 3 mA total current (30µA per capillary).


Maximum Capacity288 Samples
Minimum Sample Volume20µL (2µL of sample typically required for dilution)
ResolutionAs low as 3bp (gel dependent)
Sizing AccuracyNormally 5% or better (size dependent)
Sensitivity<50 pg/µL for smears <5 pg/µL for fragments
Light Source PowerSingle 1,000 mW LED
LED Wavelength470 nm
Emission Collection DeviceCCD detector
SoftwareFragment Analyzer System Software, ProSize Data Analysis Software
Data Export FormatMicrosoft Excel spreadsheet
Environmental ConditionsIndoor use, standard laboratory environment, 20 - 23°C
Relative Humidity Range<80% (Non-condensing)
Electrical100 - 200 VAC; 50 - 60 Hz; 15A
DimensionsMass: 38.5 Kg (85 lbs)
Size: H x W x D = 61 x 35 x 51 cm (24 x 14 x 20 in.)
CertificationsCertifications, Certified by the CSA group

Reagent Kits

Quantitative Analysis Kits

Reagent kits below are for sizing and quantitative analysis, using internal standards for accurate quantification.

DNA/NGS Fragment Analysis
Large Fragment Analysis
Genomic DNA Analysis
RNA Analysis

Qualitative/Sizing Analysis Kits

Kits below are for sizing and qualitative analysis, using a double injection of sizing markers and sample. Appropriate for genotyping or analysis of SSR’s, microsatellites, and PCR fragments.

TILLiNG/Mutation Discovery Kits

Miscellaneous Parts and Components (contact your sales person for more details)

  • (A1300-033) Modified Bottle Cap for 50mL Conical Tube
  • (A1300-034) Modified Bottle Cap for 250mL Conical Tube
  • (A1300-036) Buffer/Waste Tray Carrier
  • (M1300-025) Tray Carrier - Standard
  • (F1300-109) Tray Carrier - Fully Skirted Tray
  • (F1300-107) Tray Carrier - 12 vial strip (0.2 mL)
  • (P60-20) Fragment Analyzer 96-Well Buffer/Waste Tray
  • (P60-22) Fragment Analyzer Waste Tub
  • (FS-SMO15) Mineral Oil Dropper Bottle, 15mL
  • (GP-440-0100) Capillary Storage Solution, 100 mL

Capillary Arrays

Capillary arrays are the core of the Fragment Analyzer, affecting all aspects of electrophoresis. The array cartridges are robust, with a long lifetime, providing high quality, automated separations of nucleic acid samples. Current capillary array offerings include:

Array length is provided in centimeters with two numbers. The first number is the effective length of the capillaries - the region of the capillary that observed for separation - while the second number describes the overall length or the length of the capillary from end to end. The number of capillaries in each array directly impacts throughput, the more capillaries per array, the more samples that can be run in parallel. Array length affects both the speed of the separation and upon the separation resolution. A shorter array will provide faster electrophoresis times, while a longer array will increase separation resolution.

Use the Fragment Analyzer capillary array-kit matrix below (separation times provided in minutes) to identify which capillary array is best suited for each unique application and level of throughput.

Separation times are reported in minutes.
Quantitative Analysis
NGS LF Genomic RNA
DNF-473 DNF-474 DNF-477 DNF-464 DNF-492 DNF-493 DNF-467 DNF-487 DNF-488 DNF-470 DNF-471 DNF-472
12 Capillary Ultra-Short 25 30 35 30 30 17 31 31
12 Capillary Short 50 50 40 55 50 50 50 50 50 22 40 40
12 Capillary Long 80 80 80 80 80 80 70 70
48 Capillary Short 50 50 40 55 50 50 50 50 50 22 40 40
96 Capillary Short 50 50 40 55 50 50 50 50 50 22 40 40
96 Capillary Long 80 80 80 80 80 80 70 70
Separation times are reported in minutes.
Qualitative CRISPR
DNF-900 DNF-905 DNF-910 DNF-915 DNF-920 DNF-930 DNF-935 DNF-910CP
12 Capillary Ultra-Short 28 28 22 24 27 18 15 35
12 Capillary Short 60 60 45 50 50 30 20 50
12 Capillary Long 80 80 70 80 80 75 35
48 Capillary Short 60 60 45 50 50 30 20 50
96 Capillary Short 60 60 45 50 50 30 20 50
96 Capillary Long 80 80 70 80 80 75 35
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