Sequencers Overview iSeq 100 System MiniSeq System MiSeq i100 Series MiSeq System NextSeq 550 System NextSeq 1000 & 2000 Systems NovaSeq 6000 System NovaSeq X Series Benchtop sequencers IVD Instruments Overview MiSeqDx Instrument NextSeq 550Dx Instrument NovaSeq 6000Dx Instrument Order the iScanDx instrument Microarray Scanners Overview iScan System Automated Liquid Handlers Overview fireflyGO Trusted technology and proven performance empower scientists to explore further, with confidence. View benchtop and production-scale sequencers, compare features, and learn how to choose the right next-generation sequencing (NGS) platform for your needs. Benchtop sequencers Benchtop sequencers offer flexibility and operational simplicity. Looking for information to determine if these platforms are well-suited to your needs, and guidance selecting the right one? MiSeq i100 Series NextSeq 550 System NextSeq 1000 and 2000 Systems Small whole-genome sequencing (microbe, virus) Exome and large panel sequencing (enrichment-based) Targeted gene sequencing (amplicon-based, gene panel) Single-cell profiling (scRNA-Seq, scDNA-Seq, oligo tagging assays) Transcriptome sequencing (total RNA-Seq, mRNA-Seq, gene expression profiling) Targeted gene expression profiling miRNA and small RNA analysis DNA–protein interaction analysis (ChIP-Seq) Methylation sequencing 16S metagenomic sequencing Metagenomic profiling (shotgun metagenomics, metatranscriptomics) Cell-free sequencing and liquid biopsy analysis Explore MiSeq i100 Series Explore NextSeq 550 System Explore NextSeq 1000 and 2000 Systems Max range based on 100M flow cell specifications. 100M flow cells are available for the MiSeq i100 Plus System only. Specifications are based on a single flow cell run of the high-output flow cell using Illumina PhiX control library at supported cluster densities. NextSeq 550 Systems use different high-output flow cells. Run times includes cluster generation, sequencing, base calling, and quality scoring. Performance at the higher range of output specification is not guaranteed. Actual output is dependent on library type, user optimization, and run performance. Checkmark indicates an application or method optimized for the sequencing system. Production-scale sequencers NextSeq 1000 and 2000 Systems NovaSeq 6000 System NovaSeq X Series 10B (single flow cell) b 20B (dual flow cells) 26–35B (single flow cell) c 52–70B (dual flow cells) c,e Large whole-genome sequencing (human, plant, animal) Small whole-genome sequencing (microbe, virus) Exome and large panel sequencing (enrichment-based) Targeted gene sequencing (amplicon-based, gene panel) Single-cell profiling (scRNA-Seq, scDNA-Seq, oligo tagging assays) Transcriptome sequencing (total RNA-Seq, mRNA-Seq, gene expression profiling) Chromatin analysis (ATAC-Seq, ChIP-Seq) Methylation sequencing Metagenomic profiling (shotgun metagenomics, metatranscriptomics) Cell-free sequencing and liquid biopsy analysis Explore NextSeq 1000 and 2000 Systems Explore NovaSeq 6000 System Explore NovaSeq X Series Specifications are based on a single flow cell run of P4 flow cell using Illumina PhiX control library at supported cluster densities. P4 flow cells are available for the NextSeq 2000 System only. Specifications are based on a single flow cell run of S4 flow cell using Illumina PhiX control library at supported cluster densities. Specifications are based on Illumina PhiX control library, or a TruSeq DNA Library created with NA12878 at supported cluster densities. Performance may vary based on library type and quality, insert size, loading concentration, and other experimental factors. Run times includes cluster generation, sequencing, and base calling on a NextSeq 1000 or NextSeq 2000 System and NovaSeq 6000 System. Run times include automated onboard cluster generation, sequencing, automated post-run wash, and base calling on the NovaSeq X System. Dual flow cell runs only apply to the NovaSeq X Plus System. Checkmark indicates an application or method optimized for the sequencing system. NGS platforms for a growing sequencing community Innovative NGS platforms with proven performance and exceptional customer support expand the genomics community on a global scale. With more than 15 Illumina Solutions Centers worldwide, over 600 support personnel, 24/5 remote technical support, onsite training, instrument qualification services, and customized onboarding solutions, Illumina provides researchers with the tools and support they need to be successful in their lab. Illumina Sequencing Platforms Brochure English Arabic Brazilian Portuguese Chinese (Simplified) French German Italian Japanese Korean Spanish Brochure PDF 17 MB 10 versions Brazilian Portuguese

Chinese (Simplified) How to choose an NGS platform Find the right sequencing system by exploring important considerations for every lab. Which library prep and sequencing methods will you perform for your desired applications? What are your throughput needs? What are your goals for automating your workflow, from lab management through analysis and interpretation? Are you looking for streamlined comprehensive informatics? Technology and support Will you benefit from application flexibility, expert-level technical support, and a global community of scientists? A step-by-step guide to choosing an NGS platform This comprehensive guide will walk you through the decision process by helping you evaluate your research goals and laboratory needs. Key questions to ask before purchasing a sequencing platform NGS system categories with key factors to consider Considerations around applications and data analysis NGS buyer’s checklist NGS Workflow Finder Take the guesswork out of your next workflow. The NGS Workflow Finder provides personalized solution recommendations and resources so you can sequence with confidence. Sequencing platforms FAQ What bioinformatics pipelines are recommended for processing large-scale data sets generated by 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. What sequencing platform should I upgrade to if my current NGS system is reaching end of life? 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. What infrastructural requirements differentiate benchtop sequencers from production-scale platforms? 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 How are automated library preparation systems integrated with sequencing platforms to scale throughput? 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 . How do single-cell transcriptomics studies perform across modern ultra-high–throughput sequencing platforms? 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. Which sequencing platforms are recommended as alternatives to discontinued Illumina systems like the MiSeq and HiSeq systems? 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. Next-generation sequencing Library preparation Sequencing methods Sequencing data analysis Purchasing solutions Get up and running quickly with a rental or leasing program designed to work with your budget. Explore ecommerce and purchasing solutions for your business needs. Interested in a system demo or in speaking with someone? Get a demo of the system that you are interested in or contact a specialist to get your questions answered. Fill out a request form and we will be in touch shortly. Speak with a specialist Contact a sales representative to learn more and qualify for the Demo Program Nardone GG, Andrioletti V, Santin A, et al. A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies. Biomedicines . 2025;13(8):1949. Published 2025 Aug 9. doi:10.3390/biomedicines13081949 Satam H, Joshi K, Mangrolia U, et al. Next-Generation Sequencing Technology: Current Trends and Advancements. Biology (Basel) . 2023;12(7):997. Published 2023 Jul 13. doi:10.3390/biology12070997 Berger B, Yu YW. Navigating bottlenecks and trade-offs in genomic data analysis. Nat Rev Genet. 2023;24(4):235-250. doi:10.1038/s41576-022-00551-z Trapnell C. Revealing gene function with statistical inference at single-cell resolution. Nat Rev Genet. 2024;25(9):623-638. doi:10.1038/s41576-024-00750-w Tegally H, San JE, Giandhari J, de Oliveira T. Unlocking the efficiency of genomics laboratories with robotic liquid-handling. BMC Genomics. 2020;21(1):729. Published 2020 Oct 20. doi:10.1186/s12864-020-07137-1 Hoffmann A, Timm A, Johnson C, Rupp S, Grumaz C. Automation of customizable library preparation for next-generation sequencing into an open microfluidic platform. Sci Rep. 2024;14(1):17150. Published 2024 Jul 26. doi:10.1038/s41598-024-67950-6 Mathys H, Boix CA, Akay LA, et al. Single-cell multiregion dissection of Alzheimer's disease. Nature. 2024;632(8026):858-868. doi:10.1038/s41586-024-07606-7