SeqStudio Flex Genetic Analyzers

Flexibility, usability, connectivity, and serviceability in a mid-throughput genetic analyzer

The Applied Biosystems SeqStudio Flex Series genetic analyzers deliver the high level of Sanger sequencing and fragment analysis data quality and reliable performance that scientists need, while leveraging design improvements and technological advances for increased flexibility, easier operation, enhanced connectivity, and remote serviceability.


With a wide range of applications from simple, targeted sequencing to identification of the latest SARS variant of concern, SeqStudio Flex genetic analyzers help you to achieve freedom and peace of mind, providing extra time in your day to do what you do best: answering the big scientific questions. 

SeqStudio Flex 3D Tour


Available in both 8- and 24-capillary configurations, SeqStudio Flex Series genetic analyzers are designed with scientists in mind.

Scheduling flexibility

Four-plate capacity, continuous plate loading, and urgent sample reprioritization provide both the largest mid-throughput capacity and complete scheduling flexibility, translating into extra time in your day.

Ease of use

Easier capillary array installation, streamlined one-button start up, autocalibration, and an onboard learning center offer users of any skill level greater usability and streamlined training whether they work in a single- or multi-user environment. No instrument expert is required.

Extreme flexibility

Complete sample number, application, and run schedule flexibility.

Continuous loading of sample plates

Capillary array redesign

Designed with a “click and slide” retractor tab and enhanced detection cell housing, for improved capillary protection, easier array handling and positioning.

Seqstudio Flex capillary array

Standalone instrument

An integrated touchscreen computer with intuitive software and walk-through wizards for simplfied sample mapping, plate linking, and run setup. 

Remote setup, monitoring, and data transfer

Our Thermo Fisher Connect Platform provides enhanced flexibility and simplified collaboration by allowing users to stay connected to their instrument and data, remotely and safely, from anywhere.

Remote troubleshooting

Smart Help and Remote Support capabilities reduce instrument downtime and resolve up to 70% of issues without a service visit using immersive, real-time audio/video collaboration tools and push-button support requests.

Advanced communications and connectivity

Integrating the communication technologies of today, such as voice commands and a wide array of connectivity options, to propel laboratory efficiencies of tomorrow.

Thermo Fisher Connect Platform

Work when and where you want. Set up experiments, monitor progress, and analyze data from your mobile phone, tablet, laptop, or remote desktop using our Thermo Fisher Connect cloud-based platform.

Comprehensive software

Extract greater insight from your data using the Applied Biosystems comprehensive suite of primary and secondary analysis software with applications that include minor variant finding, microbial identification, gene editing, and next-generation sequencing confirmation.

Application diversity

Any application, any time.  Perform Sanger sequencing and fragment analysis runs on a single plate using POP-7 Polymer.

Choice of configurations

Choose between the 8- and 24-capillary configurations. If your throughput needs increase, upgrade from one configuration to the other.


SeqStudio Flex genetic analyzers deliver high-level Sanger sequencing and fragment analysis performance using capillary electrophoresis to support a diverse range of applications, including:

Targeted sequencing

NGS confirmation

Cell line authentication

Minor variant finding

Gene editing confirmation

Multiplexed PCR

Microbe or virus identification

DNA methylation analysis

SNP genotyping

Microsatellite instability (MSI) analysis

dsDNA quality control

Plasmid sequencing

Featured applications

Amplification of DNA sequences by polymerase chain reaction (PCR) remains the workhorse for almost all aspects of molecular biology and genomic research.  There is an increasing need to analyze many targets in a single sample.  However, this can be tedious by PCR, involving setting up individual reactions for each of the desired targets.  Methods that can analyze multiple sequences from a single sample would simplify workflows and conserve precious samples.  One method to address this is fragment analysis by capillary electrophoresis (CE).  CE separates amplicons based on both size and fluor in a single capillary allowing a very large number of targets to be analyzed within a single sample.  


Multiplexed PCR coupled with fragment analysis presents a tremendous opportunity to perform complex analyses with minimal expense or effort.  Experiments are limited only by the ability to design primer sets against the targets of interest.  It can therefore be adapted and utilized in nearly any scenario where detection of many target sequences in a single sample is desired.  


This example demonstrates the power of multiplexed PCR by fragment analysis using a custom panel for detecting respiratory viral pathogens.  A panel of PCR primers containing 6-FAM labeling at the 5’-end were designed to detect 12 different respiratory RNA viruses, including rhinovirus, RSV-B, influenza A H1, influenza A H3, influenza B, coronavirus HKU1, coronavirus NL63, coronavirus OC43, and coronavirus 229E, as well as SARS-CoV-2 S, N, and orf1ab, so that each organism generated a different sized amplicon.  The resulting amplicons could be separated and examined using the SeqStudio, SeqStudio 24 Flex, or 3500xL genetic analyzers.


Figure 1 – Analysis of multiple targets by multiplexed PCR and fragment analysis.  DNA targets of the RNA viruses shown above were amplified in a single reaction using a panel of 6-FAM-labelled PCR primers.  Each primer pair produces a virus-specific amplicon of a distinct size.  The grey bins were defined to detect the virus-specific targets.



Figure 2. Detection profiles of pooled genomic RNA from respiratory pathogens on the SeqStudio 24 Flex, 3500xL, and SeqStudio genetic analyzers.  The three genetic analyzers demonstrated equivalent ability to detect the multiplexed amplicons was seen on all instruments.


It is often necessary to run a quality check (QC) on a starting pool of double-stranded DNA (dsDNA) before initiating genomic analysis or continuing to the next step. For example, DNA extracted from FFPE-preserved tissue may be fragmented and too small to provide useful information, so it’s useful to know the overall size before proceeding.


The size and relative abundance of dsDNA fragments can be analyzed on the SeqStudio Flex Series genetic analyzers. In the protocol, TOTO-1, a fluorescent DNA intercalating dye, is incubated with a sample, which is run through POP7 polymer with the capillary heater turned off. (This maintains the DNA in a largely double-stranded, non-denatured state.) By comparing the resulting migration of the test fragments with the migration of known dsDNA standards, the size of the test fragments can be determined.


In this test, we assessed the performance of the SeqStudio Flex Genetic Analyzer as well as the 3500xL Genetic Analyzer in analyzing several kinds of DNA samples, including two known dsDNA standards shown in the figure. Panel A illustrates an analysis of phage lambda DNA digested with HindIII, showing the familiar pattern of eight fragments ranging from 23,130 to 125 bp. Panel B shows a mixture of the same lambda HindIII digests with phage phiX174 digested with BsuRI. In addition to the eight lambda fragments, ten more fragments ranging from 1,353 to 72 bp were detected. The profiles obtained on the SeqStudio Flex (left) and 3500xL (right) instruments were quite similar, validating the newer instrument versus the 3500 series.

Analysis of dsDNA with the SeqStudio Flex (left) and 3500xL (right) genetic analyzers.

Different DNA preparations were electrophoresed through capillaries containing POP7 at reduced temperature. Single-stranded LIZ-labelled fragments were included in the capillary. (A) Lambda HindIII digest fragments and genomic DNA from A549 cells were analyzed in different capillaries. Note the typical pattern of lambda fragments (top panels), which can be used to estimate the size of the gDNA population of about 9-23 kb (bottom panels). (B) A mixture of Lambda HindIII and phiX174 BsuRI digests and DNA extracted from an FFPE tumor sample were analyzed in different capillaries. Note the typical pattern of phage fragments (top panels); these can be used to estimate the size of the fragmented DNA (75-190 bp) and the large genomic DNA (bottom panels). In both experiments, equivalent results were obtained on both instruments.

ds DNA Quality Control Output from SeqStudio Flex and 3500 xl Genetic Analyzers

Some investigations require focused sequence information for a specific region of a genome. While genome-wide discovery tools such as NGS provide vast amounts of data over very large regions, such complex approaches are not always needed in focused research. Sanger sequencing provides a simple, cost-effective, and easy-to-interpret solution for gold-standard sequencing of a genome region. 


To demonstrate focused sequencing, we sequenced the region of the SARS-CoV-2 genome that encompasses the Spike protein and adjacent sequences, relying on previous research identifying 12 pairs of sequencing primers for the entire SARS-CoV-2 Spike gene. The Spike gene region of SARS-CoV-2 covered by the 12 overlapping amplicons extends across 5 kb.


In panel A of the figure, high-quality Sanger sequencing results (indicated by the height of the light blue bars) were obtained from nearly all 12 amplicons in both directions as shown in the figure.


These results were assembled into a single contig read of the SARS-CoV-2 Spike gene. The read quality metrics were nearly identical on all three analyzers. Consistent base-calling quality, as demonstrated here, enables Sanger sequencing to assemble the sequence of focused regions using overlapping mid-length amplicons, generating contigs that cover a locus of interest.


Sequencing the SARS-CoV-2 Spike gene by overlapping amplicons on three genetic analyzers.

1,000 copies of SARS-CoV-2 genomic RNA were reverse transcribed using Superscript VISO IV reverse transcriptase. 12 amplicons of 500–600 bp were generated using 1 µL of cDNA and amplicon pairs, cycle sequenced using BigDye Direct, and purified using BigDye Xterminator. The resulting reactions were run on the SeqStudio Flex, 3500xL, and SeqStudio genetic analyzers, and chromatograms were analyzed using SeqScanner and Genious software. Reads produced by the amplicons were mapped to each other to recapitulate the Spike gene sequence as confirmed by BLAST. (A) The read quality in each amplicon is indicated by the height of the light blue bars. Data obtained on the SeqStudio Flex instrument (shown) was highly similar to data from the 3500xL and SeqStudio instruments. The quality drop-off seen on some amplicons was also observed on the other instruments. (B) Trace score and contiguous read length and QV20+ quality values were almost identical on all three instruments.

Read quality metrics for SARS-CoV-2 Sequencing

Optimized end-to-end workflow

Thermo Fisher Scientific is committed to helping you improve data quality and drive laboratory efficiency for all your Sanger sequencing and fragment analysis applications, by providing everything you need for successful capillary electrophoresis (CE) separations from sample preparation through data analysis. We focus on quality and providing fully validated workflow solutions so that you can focus on your research.

Sanger sequencing and fragment analysis workflow graphic.

Interactive 3D tour and video

SeqStudio Flex 3D Tour

Advanced Digital Services and Support Ecosystem for your SeqStudio Flex Genetic Analyzer

See how our state-of-the-art digital support helps resolve up to 70% of cases in minutes, not days.

Introducing the Applied Biosystems SeqStudio Flex Genetic Analyzer

SeqStudio Flex Genetic Analyzer video


Superior services and support for the SeqStudio Flex Genetic Analyzer

Keep advancing with new technology. We’ve got your back.

SeqStudio Flex genetic analyzer with Service logo

Choose a service plan that’s right for you. Maximize system uptime, reduce repair costs and turnaround time, extend the life of your instrument, and help keep it running at peak performance with one of our comprehensive service plans. Choose from a variety of service options that balance your budget, productivity, uptime, and regulatory requirements. When it comes to superior services and support for your SeqStudio Flex Genetic Analyzer, we’ve got your back.

Every SeqStudio Flex Genetic Analyzer includes a one-day, on-site SmartStart Orientation to get you up and running quickly. This interactive training led by a field applications scientist (FAS) at your location provides an overview of instrument operation and maintenance, data collection and analysis software, cloud connectivity, data troubleshooting, and more.

SeqStudio Flex genetic analyzers are protected by a standard one-year factory warranty that covers all necessary costs for travel, labor, and parts. Extended-coverage service plans are available at the time of instrument purchase. Keep your laboratory running smoothly with preventive maintenance, proactive instrument monitoring, and fast response time that’s included with one of our superior service plans.


To build your personalized service quote, go to

Our most popular instrument service plan, AB Assurance, helps take the guesswork out of ensuring instrument uptime, from issue prevention to quick resolution. All parts, labor, and travel costs are included for standard repairs, and the annual planned maintenance makes it easy to keep up with instrument care. Get performance threatening issues resolved twice as fast so you can stay focused on your important work ahead of you.


Find out more about the AB Assurance Service Plan at

Instrument hardware qualifications for SeqStudio Flex genetic analyzers include installation qualification (IQ), operational qualification (OQ), and instrument performance verification (IPV) services. Our qualification specialists will partner with you to deliver timely, cost-effective, and trusted qualification services that include reliable, audit-style documentation to help ensure your SeqStudio Flex Genetic Analyzer meets regulatory requirements.


Contact an instrument qualifications specialist at

Remotely transport a service engineer into your lab in minutes using Smart Help and Remote Support.


With Smart Help, you can access onscreen technical assistance and instrument support directly from the instrument with just the push of a button. Onscreen instrument support allows you to request service and, if technical assistance is needed, interact with the service team and share log and run files to resolve issues.


Smart Help and Remote Support

Remote Support offers fast access to our service professionals using remote desktop control, reducing the need for on-site repairs that could keep customers idle for days. Immersive, real-time collaboration tools allow Technical Support to see your instrument live and interact with you on the instrument screen.


Our advanced digital service and support features can resolve up to 70% of cases in minutes, not days, so you can focus on your next scientific breakthrough.


Learn more about our on-demand tools and capabilities at

Instrument specifications

Number of capillaries

8 or 24

Number of dyes

Supports up to 8*


4-plate capacity; 96-well plates, 384-well plates, 8-tube strips 

Dimensions (W x D x H)

70 x 67.5 x 86.5 cm (27.6 x 26.6 x 34.1 in.)


115 kg (253.5 lb)

Power input

100–240 V

Internal hard drive

512 GB solid state drive (SSD)

Excitation source

505 nm solid state laser

On-instrument tracking

Radio frequency identification (RFID), internal barcode reader

Communication interface

Connect cloud-based platform; USB port for Wi-Fi dongle; 3 RJ-45 ethernet ports


Standalone; optional desktop or laptop computer available


Standard one-year warranty included; extended warranties available

SmartStart Orientation

Includes one day of onsite training by a field application scientist

Remote troubleshooting

Smart Help and Remote Support capabilities enable fast and more effective resolution of instrument issues for reduced instrument downtime

Hands-free operation

Voice command capability to perform basic instrument operations

* 8-dye capability requires a spectral calibration dye set definition file (available on request)


Ordering information

For Research Use Only. Not for use in diagnostic procedures.