Powerful viral and bacterial insights
Unrivaled simplicity, unthinkable turnaround time in your lab
Next-generation sequencing (NGS) has become an indispensable tool for microbiologists, infectious disease researchers, and public health labs.
Today, the speed and simplicity of the MiSeq i100 Series enables you to bring the power of NGS to your lab. With load-and-go reagents, shipped and stored at room temperature, the MiSeq i100 Series enables faster responses for emerging threats.
The MiSeq i100 Series provides expedited results for infectious disease and microbiology research using a custom sequencing recipe. Currently in early access and available more broadly in H2 2026, this recipe produces robust, reproducible results and reduces sequencing time by about 40% for run times around ~2.5 hours.
This approach enables researchers to move from sample to result more quickly without sacrificing data quality. When paired with Rapid RNA prep kits and onboard DRAGEN secondary analysis, the speed allows for the workflow to be completed in a single shift, which is critical to tracking outbreaks and monitoring community surveillance.
Access the simplest, fastest benchtop sequencing with the MiSeq i100 Series, providing highly accurate data for microbiome insights, novel virus tracking, and more.
The MiSeq i100 Series enables fast and reliable sequencing for various infectious disease and microbial research applications, including viral whole-genome sequencing, antimicrobial resistance marker analysis, bacterial and fungal identification, and more.
Additionally, the platforms can be highly impactful for public health surveillance tracking and monitoring of infectious agent transmission and disease spread within a community to better understand pathogen behavior and map the evolution of variants. Whether you are managing an outbreak or conducting surveillance efforts, the MiSeq i100 Series will fit your sample throughput needs.
This application note demonstrates the detection and characterization of antimicrobial resistance genes and associated bacterial pathogens in real-world wastewater samples using an NGS workflow with the Urinary Pathogen ID/AMR Enrichment Kit.
This application note demonstrates a fast, comprehensive NGS workflow that enables highly accurate detection of foodborne pathogens for effective surveillance as part of public health efforts.
In this technical note, you’ll learn how an automated NGS workflow can streamline food safety surveillance and reduce hands‑on time in the lab.
This application note demonstrates enrichment-based sequencing with the Urinary Pathogen ID/AMR Enrichment Kit for broad ARG detection without the need for culture- and growth-based phenotyping.
This application note demonstrates how the MiSeq i100 Series is part of a flexible NGS research workflow for accurate detection and characterization of HIV-1 that can be tailored to user needs.
This technical note outlines a streamlined enrichment‑based workflow that enables sensitive respiratory virus detection with the MiSeq i100 Series and onboard DRAGEN secondary analysis.
This application note demonstrates how the MiSeq i100 Series, combined with enrichment workflows, enables fast and reliable targeted sequencing for influenza detection and full-genome characterization, overcoming common amplification challenges and supporting flexible, efficient NGS workflows.
Learn how simple, scalable approaches can expand microbiome insights. This webinar highlights practical considerations for long‑amplicon (2 x 500 bp) 16S sequencing, including PCR optimization, as well as updated guidance on selecting variable regions for microbiome studies.
The MiSeq i100 Series has a streamlined workflow, from setup to data analysis, that makes benchtop sequencing faster and easier than ever. Load libraries in three simple steps and in under 20 minutes. Room temperature shipping and storage means no waiting for reagents to thaw. Preconfigured DRAGEN pipelines are included at no additional cost; they offer accurate and efficient secondary analysis onboard or in the cloud, and provide results in two hours or less for most applications while requiring minimal bioinformatics expertise.
Additionally, an intuitive interface lets you add new users and applications with ease. Whether you're tracking outbreaks, classifying novel microorganisms, or researching microbiomes, the MiSeq i100 Series provides efficient, high-quality results at an approachable price.
Introduction to starting a run
Our NGS Workflow Finder tool can help you find the right workflow for your microbiology research using predesigned workflows or by building your own.
Influenza research with the MiSeq i100 Series
In this video, Dr Seiichiro Fujisaki of Japan’s National Institute of Infectious Diseases accomplishes influenza surveillance with faster turnaround, easy workflows, and cost savings.
Producing better genomes with the MiSeq i100 Series
In this case study, the University of Zurich Institute of Medical Microbiology addresses challenges in microbial genome sequencing with the MiSeq i100 Series.
With its short sequencing run times, scalable data output, and high data quality, the MiSeq i100 is a great instrument for microbial genomes. Several aspects also make it particularly attractive for labs starting out with NGS, even in low- and middle-income countries: simple handling, ambient temperature reagent shipping, reduced need for technical support, and reduced sequencing cost.
Key microbiology applications include small whole-genome sequencing (sWGS), metagenomics, 16S rRNA sequencing, antimicrobial resistance (AMR) profiling, and targeted pathogen surveillance.
The MiSeq i100 Series benchtop sequencers are designed for microbiology. The MiSeq i100 Series delivers same-day results up to 4× faster than the original MiSeq System. It features room-temperature reagent storage, run times as short as four hours, and integrated DRAGEN secondary analysis for microbial profiling, metagenomics, and pathogen surveillance.
The MiSeq i100 Series has a streamlined workflow that includes expedited setup, room-temperature consumables, and intuitive data analysis. Workflows with validated library prep are available for pathogen detection, characterization, and surveillance. Fast sequencing run times provide results in as little as four hours, with preconfigured onboard DRAGEN analysis for same-day runs. Watch how easy it is to set-up a run on the MiSeq i100 Series.
The MiSeq i100 Series supports a range of microbial research workflows with library prep solutions using Illumina DNA Prep and panels such as Illumina Microbial Amplicon Prep for targeted pathogen surveillance, Illumina RNA Prep with Enrichment and Rapid Viral Surveillance Panel v2 for broad pathogen detection, and the Respiratory Pathogen ID/AMR Enrichment Panel (RPIP) for identifying viruses, bacteria, fungi, and antimicrobial resistance markers.
16S rRNA sequencing methods guide
Download this methods guide to learn how 16S rRNA sequencing can be used to study the impacts the microbiome has on human health and disease.
Single genome sequencing methods guide
This methods guide describes how NGS rapidly sequences microbial genomes for an understanding of behavior, host and environmental interactions, evolution, and population circulation.
Microbial sequencing solutions brochure
Download this brochure to learn how NGS can support your research goals and view workflows for microbiology and infectious disease research applications.
View this data sheet to learn how the Rapid Respiratory Pathogen ID/AMR Enrichment Panel can rapidly identify over 280 pathogens, plus antimicrobial resistance (AMR) markers, for critical public health surveillance.
Bioinformatic analysis for microbiology
Illumina offers a set of informatics tools specifically optimized for infectious disease research, public health surveillance, and microbiology.
Level up your surveillance and research with IMAP
Illumina Microbial Amplicon Prep (IMAP) offers direct-from-sample, highly multiplexed, PCR-based library preparation for microbial targets.
Talk to an expert about adopting the MiSeq i100 Series for your infectious disease and microbiology research.