Sequencing platforms

Processing massive data sets without computational bottlenecks requires bioinformatics solutions that are optimized for processing raw reads into interpretable genomic results. Data analysis pipelines, such as Illumina DRAGEN secondary analysis, are often used to perform demultiplexing, alignment, variant calling, expression analysis, and other secondary analyses, depending on the assay.

Ongoing benchmarking of bioinformatics pipelines is helpful for evaluating pipeline accuracy, precision, and reproducibility. Additionally, these evaluations assess pipeline performance in filtering sequencing artifacts and analyzing complex genomic regions, such as highly homologous regions and tandem repeats. When evaluating sequencing platforms, researchers should determine whether compatible bioinformatics pipelines integrate with high-performance computing (HPC) or cloud infrastructure, and scale with projected throughput and downstream analysis requirements.¹

Watch the DRAGEN secondary analysis webinar to learn about significant advances in machine learning (ML)-driven secondary analysis, delivering improved accuracy across germline, somatic, and multiomic workflows while preserving production‑scale performance.

Just getting started with bioinformatics? Explore our Bioinformatics for Beginners page for simplified bioinformatics solutions.

For additional information, visit our bioinformatics infrastructure and pipeline considerations and sequencing data analysis pages.

The best replacement for an end-of-life NGS system depends on numerous factors, including your current instrument, research applications, throughput and data output needs, read length and resolution requirements, workflow automation needs, and future scalability needs.²

Illumina offers numerous resources to assist with this important upgrade decision. For benchtop and production-scale sequencer upgrades, view the comparison tables on our sequencing platforms page. For additional guidance, download our sequencing platforms brochure, or visit our NGS Workflow Finder tool to determine your best workflow with resources for recommended products.

Benchtop sequencing systems typically operate from standard laboratory electrical service, are commonly paired with an uninterruptible power supply (UPS), and require relatively little laboratory space. In contrast, production-scale sequencing systems often require dedicated electrical service and additional facility infrastructure. Beyond electrical requirements, benchtop and production-scale systems also differ in their computational, environmental, and networking needs.

• Computational scaling and onboard processing: Benchtop sequencers (eg, MiSeq i100 Series) typically produce data in the gigabase (Gb) range and often use integrated or cloud-based informatics options. Production-scale systems (eg, NovaSeq X Series) can generate terabase (Tb)-scale data per run. As data output increases, additional computational infrastructure is often needed, including HPC or cloud-based solutions
• High-performance computing: Because production-scale systems generate substantially larger data sets, these systems may require enterprise-grade storage and computing solutions for high-throughput applications
• Specialized environmental control: Benchtop units can run in the ambient air conditioning of a lab, while production systems may require dedicated HVAC systems to provide additional cooling and other environmental controls depending on facility design
• Data transmission architecture: Local area networks are often sufficient for benchtop sequencing systems, whereas production-scale sequencing systems may benefit from higher-bandwidth networking, enterprise data-management and storage infrastructure, and cloud-enabled analysis workflows^3,4

Automated library preparation systems integrated into high-capacity NGS workflows with robotic liquid-handling protocols play an important role in scaling throughput. Robotic liquid handlers can provide more consistent pipetting precision and significantly reduce hands-on time during library preparation.⁵ Reducing manual sample preparation helps ensure that high-capacity instruments like the NovaSeq X Series can maintain high throughput without sample preparation becoming a bottleneck.⁶

Regardless of throughput, pipetting accuracy is critical for reproducible results. Discover our fireflyGO automated liquid handler to simplify low-throughput targeted sequencing for oncology research with automated workflows.

Learn about the benefits of automated liquid handling systems and library prep automation.

Large-scale single-cell transcriptomic studies, like single-cell RNA sequencing (scRNA-Seq), are well suited to modern ultra-high–throughput sequencing systems like the NovaSeq X Series. These sequencing systems provide the sequencing capacity, multiplexing capability, and high-quality sequencing data needed for large single-cell studies that may profile thousands to millions of cells and characterize complex cellular heterogeneity.⁷

Watch the NovaSeq X Series webinar to learn about supported methods for single cell, CRISPR, circulating RNA, and more.

Learn about scRNA-Seq methods and explore our library preparation, sequencing, data analysis, storage, and insight options.

For customers who do not require ultra-high–throughput NGS capabilities provided by the NovaSeq X Series, explore our NextSeq 1000 and 2000 Systems for scRNA-Seq.

Benchtop sequencing system alternatives:
As an alternative to the MiSeq System, consider the MiSeq i100 Series, which delivers fast run times with remarkably simple run setup and data analysis, or see all Illumina benchtop sequencers.

To find alternatives to the iSeq 100, MiniSeq, and NextSeq 500 systems, visit our benchtop sequencers page.

Production-scale sequencing system alternatives:
As an alternative to the discontinued HiSeq systems (HiSeq 1000, HiSeq 1500, HiSeq 2000, HiSeq 2500, HiSeq X Five, and HiSeq X Ten systems) and Illumina Genome Analyzer systems, consider the ultra-high–throughput NovaSeq X Series or use the production-scale sequencer comparison table on our sequencing platforms page.