Simple, fast, low-throughput Sanger sequencing and fragment analysis system

The Applied Biosystems SeqStudio Genetic Analyzer is a low-throughput, easy-to-use, and convenient benchtop system that delivers gold-standard Sanger sequencing technology and fragment analysis by capillary electrophoresis with a simple click. Just load your samples, click in the innovative all-in-one cartridge, and go.


The SeqStudio instrument is easy to use across a broad range of applications, including de novo, targeted, and plasmid Sanger sequencing, CRISPR-Cas9 genome editing confirmation, cell line authentication, and detection of single nucleotide polymorphisms (SNPs). Setup is simple and you will be ready to go in minutes. The SeqStudio Genetic Analyzer offers data quality, usability, service, and support at an affordable price.


Need higher throughput? Like the SeqStudio instrument, our  SeqStudio Flex Genetic Analyzer is an easy-to-use, flexible system for Sanger sequencing and fragment analysis, but with higher throughput.

SeqStudio 3D Tour

Learn more about financing options and programs. Learn more › 


The SeqStudio Genetic Analyzer is designed for both new and experienced users who need simple and affordable Sanger sequencing and fragment analysis, without compromising performance or quality.

Innovative all-in-one cartridge

Just load your samples, insert the cartridge, and go— no need for technical experts for set-up or maintenance

Fast turnaround

Complete your run in as little as 30 minutes

Optimized end-to-end workflow

Single polymer system allows for Sanger sequencing and fragment analysis samples to be run on the same plate in the same workflow with no reconfiguration

Touchscreen usability

The intuitive touchscreen interface simplifies plate, sample, and run setup and displays results in a choice of formats

Connectivity with Thermo Fisher Connect

Manage your run anytime, anywhere from Thermo Fisher Scientific’s Connect cloud-based platform

Comprehensive analysis software

Primary and secondary analysis software modules are available for download or through Thermo Fisher Connect

Traceability and data security module

Optional security, audit, and electronic signature (SAE) software module offers an electronic data chain of custody to help ensure integrity of your data

SmartStart customer orientation

Every SeqStudio instrument purchase includes a one-day, on-site SmartStart Orientation training course to get you up and running quickly

Learn more about these features:

The SeqStudio Genetic Analyzer uses an innovative all-in-one cartridge that includes the capillary array, anode buffer, and a reservoir containing polymer for both sequencing and fragment analysis applications. Load your samples, click in the cartridge, and go—there’s no need for expert setup or maintenance, no calibration before each run, and no installation of individual components. The reagents on the cartridge are stable on the instrument for 4–6 months, depending on the reaction size of the product.


Individual cartridges can be designated for different experimental designs or different researchers, enabling multiple users to share a single SeqStudio Genetic Analyzer. The cartridge system allows you to use only what you need and avoid unnecessary waste without sharing experimental reagents. The catridge can also be recycled.*


*Cartridge recycling available in selected regions only. For details, visit

Integrated all-in-one cartridge design.

The cartridge contains four capillaries, a detector, and a pump system that delivers polymer and buffers.

The integrated, interactive touchscreen helps you set up plates and samples, create or modify run modules, change run module priorities, and start and manage the run. View results in a choice of formats, including list view, plate view, and sequencing plots or electropherograms. Multiple views can help increase confidence in your experimental data.

SeqStudio data collection software contains an optional security, audit, and electronic signature (SAE) module that offers an electronic data chain of custody. The SAE module helps ensure the integrity of your data by defining security settings for each user account, incorporating comprehensive auditing of data objects, and requiring authentication for changes. All settings are customizable to help meet your laboratory requirements.


The SAE module supports electronic record-keeping in a way that is compliant with the US Food and Drug Administration’s Electronic Records and Signatures Rule, Part 11 of Title 21 of the Code of Federal Regulations (21 CFR Part 11). To achieve 21 CFR Part 11 compliance, your institution will also need to establish and document standard operating procedures in a compliant way.


The SAE application requires a standalone computer purchased from Thermo Fisher Scientific (desktop or laptop versions are available) and must be enabled on-site by a field service engineer.*


*If the optional SAE software module is enabled, cloud connection is disabled and remote access is unavailable.



Sanger sequencing is the gold standard for sequencing technology, enabling a high degree of accuracy, long-read capability, and the flexibility to support a diverse range of applications in many research areas. Similarly, analysis of DNA fragments enables a multitude of applications, from genotyping to bacteria identification and from plant screening to gene expression profiling.


Below are examples of applications that can be run on the SeqStudio Genetic Analyzer. For more application information, see our SeqStudio Applications page.


De novo Sanger sequencing

Targeted Sanger sequencing

Plasmid sequencing

Oncology research

Microbial species identification

Next-generation sequencing (NGS) confirmation

CRISPR-Cas9 genome editing analysis

Human cell line authentication

Single-nucleotide polymorphism (SNP) genotyping

Analysis of human copy number variation (CNV)

DNA methylation analysis

Low-level somatic variant detection and analysis

Microsatellite instability (MSI) analysis

Repeat DNA expansion

SARS-CoV-2 identification


Learn more about these applications:

There are two points in the CRISPR-Cas9 (or TALEN) genome editing workflow where the edits need to be verified. First, after the intial editing procedure, a primary screen of the resulting mixed culture can determine the percentage of cells containing the edit (editing efficiency). If the edited cells are then purified or subcloned, a secondary screen can help ensure that all cells in the subcloned population contain the edit. Sanger sequencing using the SeqStudio Genetic Analyzer can perform both of these screens as one component of Thermo Fisher Scientific’s end-to-end portfolio of genome editing tools and reagents.


In the primary screen shown in the figure below, whole-cell lysates were obtained from HEK293 cells that were edited to introduce random deletions around a target site in the HPRT or relA locus. To confirm the position of the edit, the edited cells were sequenced on the SeqStudio Genetic Analyzer and the Sanger sequencing traces were uploaded to the cloud and analyzed using the Sanger Variant Analysis module. In the screen image showing the HPRT locus, the position of the edit is clearly indicated and can be visualized by the abundant mixed-base peaks downstream of the break.

Sanger sequencing analysis of genome-edited samples at the HPRT locus using the SeqStudio Genetic Analyzer.

A mixed population of cells with a genome editing event at the human HPRT locus was analyzed using the cloud-based Sanger Variant Analysis application, which finds single-nucleotide variants common to both forward and reverse strands. On the right, the trace analysis was able to detect where the genome cleavage event occurred, producing a population of mixed sequences that can be seen to the left of the blue box in the small image on the right.

While Sanger Variant Analysis clearly showed the breakpoint and random deletions, it cannot calculate overall editing efficiency. To do so, the Sanger sequencing trace files were analyzed using Tracking of Indels by Decomposition (TIDE) software, a widely available tool for analyzing the efficiency of genome editing events. The graphs below show the spectrum and frequencies of deletions at each locus. The frequencies confirm results obtained using Invitrogen TOPO cloning followed by Sanger sequencing results of the same edited cell populations.

Analysis of two different genome editing events at the HPRT and relA loci using TIDE software. Events at the HPRT and relA loci were analyzed using TIDE software and mixed population sequencing traces generated by the SeqStudio Genetic Analyzer. The bars show the proportion of the population having the indicated number of nucleotides deleted or inserted in the forward direction (which was nearly identical to the reverse direction; data not shown). For (A) HPRT, the overall efficiency of the edit in both directions was about 80%, whereas the overall efficiency at the (B) relA locus was about 20%.

Although the study of human diseases relies heavily on dissociated human cell lines grown in culture, cells grown in vitro can be misidentified or contaminated with other unrelated cell lines, to the extent that funding agencies and journals now require cell line authentication (CLA) before awarding grants or approving publications. One way to verify the authenticity of a cell line is to identify and match its highly specific genetic “fingerprint” of variable short tandem repeats (STRs) on the SeqStudio Genetic Analyzer.


In the workflow, the IdentiFiler Plus or IdentiFiler Direct kit is used (with purified or crude DNA preparations, respectively) to amplify 16 highly variable human STR loci commonly used for verifying cell line authenticity (as well as forensic science). The fragments are analyzed on the SeqStudio instrument using GeneMapper or Microsatellite Analysis software to characterize the alleles identified by the Identifiler kits, and the results can be used to query ATCC or other STR databases to verify authenticity.

Two workflows for cell line authentication

(A) Cells can be spotted onto NUCLEIC-CARD devices, punches of the cards amplified directly using the CLA IdentiFiler Direct kit, and fragments analyzed on the SeqStudio Genetic Analyzer using GeneMapper Software 6 or the Microsatellite Analysis (MSA) cloud application. (B) Alternatively, gDNA can be purified from cell lines, amplified using the CLA IdentiFiler Plus or CLA GlobalFiler kit, and fragments analyzed on the SeqStudio instrument and GeneMapper Software 6 or the MSA cloud application.

In this test of the ability of the SeqStudio Genetic Analyzer to detect contaminating cells, a population of M4A4GFP cells was spiked with varying amounts of HeLa cells and analyzed using the IdentiFiler Direct kit (workflow B). HeLa cell-specific alleles could be detected even if HeLa cells made up only 10% of the population.

Analysis of cell line contamination on the SeqStudio Genetic Analyzer.

HeLa cells and M4A4GFP cell suspensions were diluted to 5 x 105 cells/mL, mixed in the indicated proportions, and spotted onto a NUCLEIC-CARD Sample Collection Device. Results showed that contaminating HeLa cells can be detected with high (>80%) confidence on the SeqStudio instrument if they make up as little as 20% of a population, and some alleles unique to HeLa can be detected if they make up as little as 10% of a population.

Optimized end-to-end workflow

The SeqStudio Genetic Analyzer can perform both Sanger sequencing and fragment analysis runs on the same plate within the same workflow. Gain flexibility in your laboratory schedule and help maximize your time by removing the need to batch samples.

Dual workflow.

The SeqStudio Genetic Analyzer can perform simultaneous Sanger sequencing and fragment analysis runs on the same plate.

We offer a complete product portfolio for every step of the Sanger sequencing and fragment analysis workflows. For Sanger sequencing, this includes amplifying the DNA template, PCR cleanup, cycle sequencing, sequencing cleanup, on‑instrument consumables, and data analysis. For fragment analysis, this includes DNA extraction, PCR amplification, on‑instrument consumables, and data analysis.

Videos, webinars, and demos




Number of capillaries


Number of dyes


Sample format

96-well standard plate and standard 8-tube strips


  • Sanger sequencing (resequencing NGS confirmation, indels, heterozygote detection, minor variant detection, microbial identification, genome editing validation)
  • Fragment analysis (microsatellite analysis, compatible with MLPA, Applied Biosystems SNaPshot applications, cell line authentication

Secondary analysis software included

  • Sequence Analysis Software
  • SeqScape Software
  • Variant Reporter Software
  • GeneMapper Software
  • Minor Variant Finder Software
  • Sequencing Analysis Modules (Quality Check, Variant Analysis, and Next-Generation Confirmation) on Connect platform
  • Fragment Analysis Modules (Peak Scanner and Microsatellite Analysis) on Connect platform
  • SeqScreener Gene Editing App


Included (1 year)

In-lab application training




Capillary array length

28 cm (works with POP-1 polymer to resolve short and long reads)

Polymer type

Universal polymer POP-1 (for performing sequencing and fragment analysis)

Maximum number of injections/reactions

Up to 125 injections/500 reactions or sample (A33671)
Up to 250 injections/1000 reactions or samples (A41331)

On-instrument shelf life

4 or 6 months after opening

Cartridge recycling

Available in most regions

On-instrument tracking

RFID (radio frequency identification)



Superior services and support for the SeqStudio Genetic Analyzer

Choose a service plan that’s right for you. Help 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 Genetic Analyzer, we’ve got your back.


SmartStart Orientation enables your success

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


Comprehensive warranty and service plans protect your investment

SeqStudio Genetic Analyzers are protected by a standard one-year factory warranty that covers 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.


Service plan overview

Service aspect

AB Maintenance (Plus) plan

AB Assurance plan

AB Complete plan

On-site response time

Target 2 business days*

Guaranteed 2 business days*

Guaranteed next business day*

Scheduled on-site planned maintenance

Remote instrument diagnostics

Parts, labor, and travel

10% discount (US only)

Priority access to remote service engineer


Requalification, post-planned maintenance (PM) and critical repairs



Troubleshooting by field application scientist



*Response times vary by region


All service plans include scheduled planned maintenance and the latest software updates, enabling optimum reliability. Service plans help keep operating costs predictable, as parts, labor, and engineer travel are included or discounted.

Qualification services help ensure regulatory compliance

Instrument hardware qualifications for SeqStudio 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 Genetic Analyzer meets regulatory requirements.


Ordering information

*This offer is only available to customers in Canada and the United States (excluding Puerto Rico) who acquire manufactured products and service plans from Thermo Fisher Scientific or its affiliates. Some exclusions may apply. Offer will apply to approved applicants and who sign a Thermo Fisher Financial Services contract that is received by Thermo Fisher Financial Services no later than December 31, 2022. Customers must submit a Thermo Fisher Financial Services credit application and be approved for credit. Interest rates vary based on credit rating. Not all buyers may qualify for credit approval or promotional rate. Determination of eligibility is at the sole discretion of Thermo Fisher Financial Services credit committee. Financing shall be subject to contract terms and conditions. Cannot be combined with other discounts or promotions.  Offer void where prohibited, licensed or restricted by federal, state, provincial, or local laws or regulation or agency/institutional policy. Offer subject to change without notice. Other restrictions may apply.