Benchtop sequencers are compact and adaptable devices that create new pathways for small labs to impact both research and clinical settings significantly. These sequencers operate at the point of need, providing rapid results, which is critical when patient care and outcomes are at stake. When supported by appropriate tools and resources, such as a Laboratory Information Management System (LIMS System) like Sapio Sciences, these benchtop sequencers can deliver results more efficiently, leading to better patient outcomes and a more comprehensive reach of genomic research. Tools like Sapio LIMS allow smaller labs to collaborate, share findings, and advance genomic research on a broader scale, overcoming the traditional constraints of larger, costlier platforms requiring specialized infrastructure and large teams. By combining the power of benchtop sequencers and comprehensive data management, smaller labs can now contribute to significant breakthroughs in genomics with greater agility and cost-effectiveness.

Advantages of Benchtop Sequencers

Benchtop sequencers are designed to be compact, portable, cost-effective, versatile, and simple to use. Their flexibility allows them to support various applications, from short-read to long-read sequencing and even real-time sequencing. They are transportable, save time, and ultimately contribute to saving lives by enabling quicker diagnoses and treatments. These characteristics make them ideal for various environments, including smaller labs, academic institutions, and field studies. There are multiple types of sequencing for these devices, which all have their advantages. These include: 

Short-Read Sequencing

Short-read sequencing, typically represented by platforms like Illumina MiSeq and MiniSeq, involves reading DNA fragments in shorter lengths, usually between 50 and 300 base pairs. The key advantages of these platforms are:

  1. High Accuracy: They deliver high-precision results ideal for clinical diagnostics, targeted gene sequencing, and whole-genome sequencing.
  2. High Throughput: These sequencers can generate large volumes of data relatively quickly, allowing for large-scale studies and multiplexing.
  3. Diverse Applications: Short-read sequencing supports various applications, including exome sequencing, RNA-seq, ChIP-seq, and more.
  4. Cost-Effectiveness: With high throughput and versatility, short-read sequencing can be more cost-effective for large-scale projects.

Long-Read Sequencing

Popular long-read sequencing platforms, including sequencers such as Oxford Nanopore’s MinION and PacBio’s Sequel II/IIe. These sequencers offer longer-read sequences ranging from thousands to tens of thousands of base pairs. Long-read sequencing has grown in popularity due to its ability to detect complex structural variations and perform de novo genome assembly. The key benefits of using these sequencers include:

  1. Detection of Structural Variants: Long-read sequencing is perfect for identifying large-scale genomic changes like insertions, deletions, and translocations, which can be tricky to detect using short-read platforms.
  2. De Novo Genome Assembly: The longer reads allow for assembling novel genomes with fewer gaps, providing a more complete picture of what you are investigating.
  3. Analysis of Repetitive Regions: Long-read sequencing can cover highly repetitive regions and complex genomic areas, such as centromeres and telomeres, offering more comprehensive insights.

Real-Time Sequencing

Oxford Nanopore’s technology currently dominates the real-time sequencing area, allowing researchers to analyze DNA as it is sequenced in real-time. This provides significant advantages and will be an area that will grow in the near future, including:

  1. Rapid Results: Real-time sequencing enables researchers to get results in hours, critical for clinical diagnostics and outbreak monitoring.
  2. Field Flexibility: Real-time sequencers, like the MinION, are portable and ideal for field studies, allowing for on-site analysis without complex lab infrastructure. This flexibility is essential for studying infectious diseases, environmental changes, and biodiversity, and it also enables vital resources to areas that need more capabilities to have more extensive sequencing facilities and limited resources.
  3. Adaptive Sampling: Researchers can adjust sequencing in real-time based on initial results, focusing on critical areas and reducing off-target sequencing.

Enhancing Benchtop Sequencers with Sapio LIMS

Sapio’s LIMS can significantly enhance the efficiency and effectiveness of benchtop sequencers by streamlining operations, automating processes, and improving data management. This can enable users to make a big impact with smaller sequencers. Some critical areas where Sapio LIMS can make a difference quickly after implementation:

  1. Centralized Data Management: A LIMS System provides a centralized repository for all data generated by benchtop sequencers, facilitating easy tracking, retrieval, and analysis. This centralization also aids in data sharing and collaboration across labs, sites, or continents.
  2. Streamlined Workflow Automation: A LIMS can automate various aspects of the sequencing workflow, reducing manual errors and speeding up processes. Integrating with benchtop sequencers, a LIMS can automatically capture sequencing data, track progress, and generate reports.
  3. Enhanced Quality Control: A LIMS ensures quality control by tracking metadata, sample preparation details, and sequencing parameters. This helps maintain high standards and provides reliable results across all sites.
  4. Seamless Integration with Other Systems or Instruments: A LIMS can integrate with other lab systems and instruments, allowing for smooth data transfer and analysis. This seamless integration streamlines operations and reduces data redundancy.
  5. Improved Collaboration and Communication: A LIMS enables secure research collaboration, facilitating joint projects and real-time communication. This fosters a more collaborative research environment. Sapio LIMS’s collaboration aspect enables researchers to work together with the same experiment template simultaneously, which is ideal for training and sharing information. 
  6. Efficient Compliance and Audit Trails: A LIMS helps labs meet regulatory standards and maintain accurate audit trails, essential for clinical and diagnostic applications.
  7. Flexible and Scalable Solutions: This scalability of the Sapio LIMS allows for growth without compromising efficiency.


Benchtop sequencers have revolutionized genomic research by offering a versatile range of sequencing options within compact devices. These sequencers have democratized genomics, making it more accessible for smaller labs and academic institutions to contribute to significant breakthroughs. Real-time sequencing adds flexibility, allowing researchers to adapt quickly and obtain results in a shorter timeframe. With a robust Laboratory Information Management System (LIMS) like Sapio’s, benchtop sequencers become even more efficient, enabling centralized data management, automated workflows, and enhanced quality control. This relationship between benchtop sequencers and LIMS can drive innovation in genomics, which ultimately has the potential to increase the pace of personalized medicine and, in turn, improve patient outcomes.