MiSeq i100 System

The MiSeq i100 Series delivers our fastest run times yet, breakthrough simplicity, and significant sustainability advancements to empower every lab, everywhere

The new standard in benchtop sequencing speed and simplicity

Same-day (and same-shift) results are now possible. The MiSeq i100 and MiSeq i100 Plus Systems provide results 4× faster than the MiSeq System, with sequencing run times as fast as four hours.

With the expanded output offered by the MiSeq i100 Series, you can increase sample throughput, perform deeper sequencing, and gain more insights for a wide range of applications faster than ever. XLEAP-SBS chemistry on the MiSeq i100 Series eliminates thawing requirements so reagents can be used whenever your sample is ready.

The MiSeq i100 Series makes NGS simpler than ever

Every aspect of the MiSeq i100 Series workflow is noticeably simplified, from setup to data analysis. Whether you are new to sequencing or an experienced user, you’ll appreciate the streamlined operations. Run setup requires only three steps and can be completed in less than 20 minutes.

Integrated cartridges simplify library loading and eliminate the need for washes between runs, improving sequencing efficiency.

Generate data analysis summaries in two hours or less for most applications by accessing preconfigured DRAGEN pipelines, either onboard or in the cloud.

Ground-breaking sustainability innovations

In addition to breakthrough advancements in system design, XLEAP-SBS chemistry, and integrated data analysis, the MiSeq i100 Series is optimized to reduce environmental impact. Key innovations, such as an 85% reduction in packaging waste* and a 35% reduction in the total carbon footprint, plus room-temperature ship-and-store consumables, deliver remarkable sustainability and user experience benefits.

Trusted for over a decade, the MiSeq System has been shipped to over 10,000 customers globally, and has been cited in over 160,000 peer-reviewed publications.

Building on our extensive expertise, Illumina has a relentless commitment to innovation and building future next-generation sequencing (NGS) capabilities and applications. The MiSeq i100 Series demonstrates our commitment to increasing access to genomics technology by continuing to deliver faster, simpler sequencing.

See how the MiSeq i100 Series is setting the standard for simplicity, usability, and speed of benchtop sequencing from Illumina.

Illumina provides a world-class support team composed of experienced scientists who are experts in library prep, sequencing, and analysis. This exceptional technical support is available via phone five days a week or online 24/7, worldwide, and in multiple languages, with rapid response time near most major metropolitan areas.

To help you get high-quality results on Illumina technology even faster, we offer instructor-led or hands-on courses and web-based training options.

With both supported workflows and a large ecosystem of choices, Illumina products are available for every step of the MiSeq i100 Series workflow.

The MiSeq i100 Series offers highly accurate quality data for various applications, including oncology, infectious disease, and microbiology studies.

Are you new to sequencing or considering your first instrument?

These resources cover key topics in NGS designed for beginners. We'll provide tutorials, guide you through the workflow and planning your first experiment.

Get up and running quickly with a rental or leasing program designed to work with your budget. Choose from several options to obtain financing, including instrument leasing, instrument rental, and reagent rental.

Illumina Proactive is a secure and remote instrument performance and support service. Our field support team can identify risks before your run, perform reagent lot tracking, maximize uptime, and improve lab efficiency. Register for a MyIllumina account to get started.

Key Features

• Prepare libraries: With the MiSeq i100 Series, libraries are loaded in three simple steps and in under 20 minutes.
• Sequence: Increase efficiency with XLEAP-SBS chemistry and streamlined operations, including onboard denaturation and clustering to obtain fast, high-quality data.
• Analyze data: Obtain accurate and efficient secondary analysis with preconfigured DRAGEN pipelines onboard or in the cloud, generating results in two hours or less for most applications.
• Interpret results: Gain insights and drive discovery with cloud-based tertiary analysis solutions for select workflows.
• Room-temperature reagents: The reagents are shipped and stored at room temperature and ready to use immediately, expediting sequencing setup.
• Index-first sequencing: Experience faster demultiplexing and real-time run management with index-first sequencing.
• XLEAP-SBS chemistry: XLEAP-SBS chemistry is our fastest, most robust, highest-quality sequencing chemistry to date.
• Ready-to-use cartridge: Flow cells and fluidics integrated in a single cartridge simplify setup and eliminate washes.
• Streamlined bioinformatics: Predesigned DRAGEN pipelines onboard the MiSeq i100 Series and in the cloud streamline data analysis.

Applications

• oncology
• infectious disease
• microbiology studies
• Transcriptomics
• Microbial genomics
• Targeted gene sequencing
• Quality control
• 3’ gene expression
• Targeted RNA panel
• mRNA-Seq
• Total RNA-Seq
• Pathogen detection
• 16S amplicon sequencing
• Shallow shotgun metagenomics
• Shotgun metagenomics

Specifications

MiSeq i100 Series specifications
Output range	1.5–30 Gb
Paired-end reads per run	10–200M
Max read length	2 × 500 bp
Run time	~4–24 hr
MiSeq i100 Series
Run time (range)	~4–24 hr
NextSeq 1000 and 2000 Systems
Run time (range)	8–44 hr
MiSeq i100 Series
Max output	30 Gb
NextSeq 1000 and 2000 Systems
Max output	540 Gb
MiSeq i100 Series
Max reads per run	100 million single reads; 200 million paired-end reads
NextSeq 1000 and 2000 Systems
Max reads per run	1.8 billion single reads; 3.6 billion paired-end reads
MiSeq i100 Series
Informatics options	On-instrument: Custom menu of DRAGEN analysis pipelines; Cloud: Broad menu of DRAGEN analysis applications available on BaseSpace Sequence Hub and Illumina Connected Analytics; On-premises: Broad menu of DRAGEN analysis applications
NextSeq 1000 and 2000 Systems
Informatics options	On-instrument: Custom menu of DRAGEN analysis pipelines; Cloud: Broad menu of DRAGEN analysis applications available on BaseSpace Sequence Hub and Illumina Connected Analytics; On-premises: Broad menu of DRAGEN analysis applications
Output per flow cell for various read lengths — 5M
1 × 100 bp	—
Output per flow cell for various read lengths — 25M
1 × 100 bp	2.5 Gb
Output per flow cell for various read lengths — 50M
1 × 100 bp	5 Gb
Output per flow cell for various read lengths — 100M
1 × 100 bp	10 Gb
Output per flow cell for various read lengths — 5M
2 × 150 bp	1.5 Gb
Output per flow cell for various read lengths — 25M
2 × 150 bp	7.5 Gb
Output per flow cell for various read lengths — 50M
2 × 150 bp	15 Gb
Output per flow cell for various read lengths — 100M
2 × 150 bp	30 Gb
Output per flow cell for various read lengths — 5M
2 × 300 bp	3 Gb
Output per flow cell for various read lengths — 25M
2 × 300 bp	15 Gb
Output per flow cell for various read lengths — 50M
2 × 300 bp	30 Gb
Output per flow cell for various read lengths — 100M
2 × 300 bp	—
Output per flow cell for various read lengths — 5M
2 × 500 bp	—
Output per flow cell for various read lengths — 25M
2 × 500 bp	25 Gb
Output per flow cell for various read lengths — 50M
2 × 500 bp	—
Output per flow cell for various read lengths — 100M
2 × 500 bp	—
Reads passing filter per flow cell — 5M
Single reads	5M
Reads passing filter per flow cell — 25M
Single reads	25M
Reads passing filter per flow cell — 50M
Single reads	50M
Reads passing filter per flow cell — 100M
Single reads	100M
Reads passing filter per flow cell — 5M
Paired-end reads	10M
Reads passing filter per flow cell — 25M
Paired-end reads	50M
Reads passing filter per flow cell — 50M
Paired-end reads	100M
Reads passing filter per flow cell — 100M
Paired-end reads	200M
Quality scores — 5M
1 × 100 bp	≥ 90% of bases higher than Q30
Quality scores — 25M
1 × 100 bp	≥ 90% of bases higher than Q30
Quality scores — 50M
1 × 100 bp	≥ 90% of bases higher than Q30
Quality scores — 100M
1 × 100 bp	≥ 90% of bases higher than Q30
Quality scores — 5M
2 × 150 bp	≥ 90% of bases higher than Q30
Quality scores — 25M
2 × 150 bp	≥ 90% of bases higher than Q30
Quality scores — 50M
2 × 150 bp	≥ 90% of bases higher than Q30
Quality scores — 100M
2 × 150 bp	≥ 90% of bases higher than Q30
Quality scores — 5M
2 × 300 bp	≥ 85% of bases higher than Q30
Quality scores — 25M
2 × 300 bp	≥ 85% of bases higher than Q30
Quality scores — 50M
2 × 300 bp	≥ 85% of bases higher than Q30
Quality scores — 100M
2 × 300 bp	≥ 85% of bases higher than Q30
Quality scores — 5M
2 × 500 bp	≥ 85% of bases higher than Q30
Quality scores — 25M
2 × 500 bp	≥ 85% of bases higher than Q30
Quality scores — 50M
2 × 500 bp	≥ 85% of bases higher than Q30
Quality scores — 100M
2 × 500 bp	≥ 85% of bases higher than Q30
Run time — 5M
1 × 100 bp	—
Run time — 25M
1 × 100 bp	~ 4 hr
Run time — 50M
1 × 100 bp	~ 4.5 hr
Run time — 100M
1 × 100 bp	~ 5 hr
Run time — 5M
2 × 150 bp	~ 7 hr
Run time — 25M
2 × 150 bp	~ 7 hr
Run time — 50M
2 × 150 bp	~ 7.5 hr
Run time — 100M
2 × 150 bp	~ 8 hr
Run time — 5M
2 × 300 bp	~ 15 hr
Run time — 25M
2 × 300 bp	~ 15 hr
Run time — 50M
2 × 300 bp	~ 15.5 hr
Run time — 100M
2 × 300 bp	—
Run time — 5M
2 × 500 bp	—
Run time — 25M
2 × 500 bp	~ 24 hr
Run time — 50M
2 × 500 bp	—
Run time — 100M
2 × 500 bp	—
Estimated sample throughput for key applications — Reads per sample
Transcriptomics – 3’ gene expression	1−5M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Transcriptomics – 3’ gene expression	1−5
Estimated sample throughput for key applications — Number of samples per flow cell: 25M
Transcriptomics – 3’ gene expression	5−25
Estimated sample throughput for key applications — Number of samples per flow cell: 50M
Transcriptomics – 3’ gene expression	10−50
Estimated sample throughput for key applications — Number of samples per flow cell: 100M
Transcriptomics – 3’ gene expression	25−100
Estimated sample throughput for key applications — Reads per sample
Transcriptomics – Targeted RNA panel	1−5M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Transcriptomics – Targeted RNA panel	1−5
Estimated sample throughput for key applications — Number of samples per flow cell: 25M
Transcriptomics – Targeted RNA panel	5−25
Estimated sample throughput for key applications — Number of samples per flow cell: 50M
Transcriptomics – Targeted RNA panel	10−50
Estimated sample throughput for key applications — Number of samples per flow cell: 100M
Transcriptomics – Targeted RNA panel	25−100
Estimated sample throughput for key applications — Reads per sample
Transcriptomics – mRNA-Seq	10−25M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Transcriptomics – mRNA-Seq	—
Estimated sample throughput for key applications — Number of samples per flow cell: 25M
Transcriptomics – mRNA-Seq	1−2
Estimated sample throughput for key applications — Number of samples per flow cell: 50M
Transcriptomics – mRNA-Seq	1−5
Estimated sample throughput for key applications — Number of samples per flow cell: 100M
Transcriptomics – mRNA-Seq	1−10
Estimated sample throughput for key applications — Reads per sample
Transcriptomics – Total RNA-Seq	50M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Transcriptomics – Total RNA-Seq	—
Estimated sample throughput for key applications — Number of samples per flow cell: 25M
Transcriptomics – Total RNA-Seq	—
Estimated sample throughput for key applications — Number of samples per flow cell: 50M
Transcriptomics – Total RNA-Seq	1
Estimated sample throughput for key applications — Number of samples per flow cell: 100M
Transcriptomics – Total RNA-Seq	1−2
Estimated sample throughput for key applications — Reads per sample
Microbial genomics – Pathogen detection	0.5−1M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Microbial genomics – Pathogen detection	1−10
Estimated sample throughput for key applications — Number of samples per flow cell: 25M
Microbial genomics – Pathogen detection	1−50
Estimated sample throughput for key applications — Number of samples per flow cell: 50M
Microbial genomics – Pathogen detection	1−100
Estimated sample throughput for key applications — Number of samples per flow cell: 100M
Microbial genomics – Pathogen detection	1−200
Estimated sample throughput for key applications — Reads per sample
Microbial genomics – 16S amplicon sequencing	0.1−0.2M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Microbial genomics – 16S amplicon sequencing	1−50
Estimated sample throughput for key applications — Number of samples per flow cell: 25M
Microbial genomics – 16S amplicon sequencing	1−250
Estimated sample throughput for key applications — Number of samples per flow cell: 50M
Microbial genomics – 16S amplicon sequencing	1−384
Estimated sample throughput for key applications — Number of samples per flow cell: 100M
Microbial genomics – 16S amplicon sequencing	1−384
Estimated sample throughput for key applications — Reads per sample
Microbial genomics – Shallow shotgun metagenomics	0.5−10M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Microbial genomics – Shallow shotgun metagenomics	1−10
Estimated sample throughput for key applications — Number of samples per flow cell: 25M
Microbial genomics – Shallow shotgun metagenomics	1−12
Estimated sample throughput for key applications — Number of samples per flow cell: 50M
Microbial genomics – Shallow shotgun metagenomics	1−25
Estimated sample throughput for key applications — Number of samples per flow cell: 100M
Microbial genomics – Shallow shotgun metagenomics	1−50
Estimated sample throughput for key applications — Reads per sample
Microbial genomics – Shotgun metagenomics	10−25M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Microbial genomics – Shotgun metagenomics	—
Estimated sample throughput for key applications — Number of samples per flow cell: 25M
Microbial genomics – Shotgun metagenomics	1−2
Estimated sample throughput for key applications — Number of samples per flow cell: 50M
Microbial genomics – Shotgun metagenomics	1−5
Estimated sample throughput for key applications — Number of samples per flow cell: 100M
Microbial genomics – Shotgun metagenomics	1−10
Estimated sample throughput for key applications — Reads per sample
Microbial genomics – Small WGS	0.5M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Microbial genomics – Small WGS	1−10
Estimated sample throughput for key applications — Number of samples per flow cell: 25M
Microbial genomics – Small WGS	1−50
Estimated sample throughput for key applications — Number of samples per flow cell: 50M
Microbial genomics – Small WGS	1−100
Estimated sample throughput for key applications — Number of samples per flow cell: 100M
Microbial genomics – Small WGS	1−200
Estimated sample throughput for key applications — Reads per sample
Targeted gene sequencing – Amplicon-based	0.1−50M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Targeted gene sequencing – Amplicon-based	1−5
Estimated sample throughput for key applications — Number of samples per flow cell: 25M
Targeted gene sequencing – Amplicon-based	1−250
Estimated sample throughput for key applications — Number of samples per flow cell: 50M
Targeted gene sequencing – Amplicon-based	1−384
Estimated sample throughput for key applications — Number of samples per flow cell: 100M
Targeted gene sequencing – Amplicon-based	1−384
Estimated sample throughput for key applications — Reads per sample
Targeted gene sequencing – Enrichment-based	0.1−50M
Estimated sample throughput for key applications — Number of samples per flow cell: 5M
Targeted gene sequencing – Enrichment-based	1−50

Documents

• MiSeq i100 specifications
• MiSeq i100 Series – Product brochure
• Sequencing systems brochure
• Reads passing filter (technical note)
• MiSeq i100 Series – Index-first sequencing (technical note)
• MiSeq i100 Series sustainability infographic
• Producing better genomes with the MiSeq i100 Plus System

Related Products

• NextSeq 1000 and 2000 Systems
• MiSeq i100 Series Reagent Kits
• Illumina DNA Prep
• Illumina RNA Prep with Enrichment
• Illumina Microbial Amplicon Prep