MiSeq i100 Series applications and methods

Simplest workflow, fastest results

Perform a wide range of applications on our fastest, simplest benchtop sequencer, with flexible output and read-to-use workflows optimized for novice users

Scientist starting a sequencing workflow on MiSeq i100 System

Key applications and methods

Whether you use our predesigned supported workflows or build your own, we have options to support every step of the workflow.

Supported sample-to-analysis workflows: The MiSeq i100 and MiSeq i100 Plus Systems offer supported sample-to-analysis workflows for various methods. These workflows include library prep kits, panels, sequencing on the MiSeq i100 Series, DRAGEN secondary analysis, and data interpretation (where applicable). Additional workflows will be supported in the future.

Microbiome and pathogen discovery

Targeted, culture-free sequencing of complex biological samples to identify and compare bacterial taxa present in microbial communities.

Supported sample-to-analysis workflow

16S amplicon sequencing

Culture-free NGS method that identifies microbes in complex samples. A cost-effective, culture-free method for identification of bacterial strains not found using traditional methods.

Shotgun DNA sequencing

Functional characterization of all microbial genomes present in a complex sample. Fast, integrated library prep completes in < 4 hr with minimal hands-on time.

1
Library prep
3
Data analysis & interpretation

Shotgun RNA sequencing

Functional quantification of all coding and noncoding RNAs present in complex samples. Efficient depletion of ribosomal RNA and human globin mRNA across multiple species and sample types.

Single-genome microbial sequencing

Microbial sequencing and analysis of a single, known organism, whether from an isolated, cultured bacterial colony or a primary sample being surveilled for a determined pathogen of interest.

Supported sample-to-analysis workflow

Microbial WGS

Comprehensive method for mapping, finishing, or comparing microbial genomes for deep insights. Fast, integrated library prep completes in < 4 hr with minimal hands-on time.

1
Library prep
3
Data analysis & interpretation

DRAGEN sWGS onboard MiSeq i100

Resources

Tuberculosis ID and drug resistance characterization

Targeted NGS panel for identification of Mycobacterium tuberculosis complex strains. Prepare sequencing libraries from as little as 9 pg of DNA.

Supported sample-to-analysis workflow

SARS-CoV-2 sequencing

Comprehensive, amplicon-based assay for characterization of the SARS-CoV-2 virus. Low- to-mid-throughput NGS assay enables labs of any size to surveil novel SARS-CoV-2 variants.

1
Library prep
3
Data analysis & interpretation

Supported sample-to-analysis workflow

Influenza sequencing

Multiplexed, amplicon-based assay for WGS of influenza A/B viruses for public health surveillance and research studies. Automation-friendly RT-PCR and tagmentation-based workflow for influenza A/B analyses.

1
Library prep
3
Data analysis & interpretation

Supported sample-to-analysis workflow

Flexible microbial sequencing

Custom, user-defined targeted sequencing for identification and characterization of specific microbes of interest. Compatible with custom, published, or commercially available primer sets targeting microbes of interest.

3
Data analysis & interpretation

Multipathogen sequencing

Multipathogen sequencing via amplicon-based NGS involves analyzing genomic regions of interest with ultradeep sequencing of PCR amplicons. Enables full characterization of viruses.

Supported sample-to-analysis workflow

Viral public health threat sequencing

Obtain WGS data for characterization of a broad range of viruses, including SARS-CoV-2, influenza, and poliovirus. Perform concurrent analysis of RNA and DNA viruses compatible with a range of sample types.

1
Library prep
3
Data analysis & interpretation

DRAGEN Microbial Enrichment Plus onboard MiSeq i100

Common respiratory virus sequencing

Targeted, streamlined detection of common respiratory viruses, such as SARS-CoV-2 and influenza A/B. Target enrichment through hybrid–capture methods provides highly sensitive detection without the need for high read depth.

1
Library prep
3
Data analysis & interpretation

DRAGEN Microbial Enrichment Plus onboard MiSeq i100

Supported sample-to-analysis workflow

Respiratory pathogen and AMR sequencing

NGS-based panel that targets > 280 respiratory pathogens and > 2000 antimicrobial resistance markers with streamlined, sample-to-results workflow.

3
Data analysis & interpretation

DRAGEN Microbial Enrichment Plus onboard MiSeq i100

Supported sample-to-analysis workflow

Urinary tract pathogen and AMR sequencing

NGS-based panel that targets > 170 uropathogens and > 3700 antimicrobial resistance markers with streamlined, sample-to-results workflow.

1
Library prep
3
Data analysis & interpretation

DRAGEN Microbial Enrichment Plus onboard MiSeq i100

Targeted cancer sequencing

Targeted cancer sequencing, comprising a focused selection of genes associated with specific cancer types or pathways, complement broader genomic profiling approaches and offer users multiple options to interrogate and understand cancer biology.

Supported sample-to-analysis workflow

Multicancer CNV and fusion analysis

Targeted detection of multiple variants, including CNVs and gene fusions. Single-tube SLIMamp workflow provides fast library prep and turnaround time.

1
Library prep

Library prep

SLIMamp Amplicon Prep

3
Data analysis & interpretation

Data analysis

Amplicon Pillar PiVAT

Supported sample-to-analysis workflow

Myeloid cancer gene detection

Targeted interrogation of 58 genes of interest highly relevant to myeloid cancers. Single-tube SLIMamp workflow provides fast library prep and turnaround time.

1
Library prep

Library prep

SLIMamp Amplicon Prep

3
Data analysis & interpretation

Data analysis

DRAGEN DNA

Amplicon Pillar PiVAT

Supported sample-to-analysis workflow

Solid tumor fusion detection

Focused detection of multiple gene rearrangement regions of interest across solid tumor types. Single-tube SLIMamp workflow provides fast library prep and turnaround time.

1
Library prep

Panel

Pillar oncoReveal Multi-Cancer RNA Fusion v2 Panel

Library prep

SLIMamp Amplicon Prep

3
Data analysis & interpretation

Data analysis

DRAGEN DNA

Amplicon Pillar PiVAT

Cancer gene expression and fusion detection

Comprehensive assessment of 1385 cancer-related RNA transcripts. In-depth and cost-effective assessment of cancer-related transcripts across most sample types, including FFPE samples.

1
Library prep

Library prep

SLIMamp Amplicon Prep

3
Data analysis & interpretation

Data analysis

Amplicon Pillar PiVAT

Supported sample-to-analysis workflow

BRCA gene sequencing

Targeted sequencing panel for BRCA1/2 mutations and copy number variations. Single-tube SLIMamp workflow provides fast library prep and turnaround time.

1
Library prep

Library prep

SLIMamp Amplicon Prep

3
Data analysis & interpretation

Data analysis

Data interpretation

Supported sample-to-analysis workflow

Hereditary cancer gene sequencing

Targeted sequencing panel that assesses germline mutations across 113 genes and 125 SNPs associated with genetic cancer risk predispostion. Expert-defined content developed with input from key opinion leaders.

3
Data analysis & interpretation

Data analysis

Data interpretation

Supported sample-to-analysis workflow

B-cell and/or T-cell receptor sequencing

Analyze B- or T-cell receptor diversity and clonal expansion to gain insights into the adaptive immune system. Flexible library prep from a wide range of RNA input amounts from as little as 10 ng up to 3 μg of RNA.

3
Data analysis & interpretation

Takara Data Analysis

Related content

Benchtop applications ebook

Download this eBook to learn how benchtop sequencers support a broad range of applications while delivering exceptional data quality and accuracy.

NGS library prep

Experience the quality, precision, and ease of use in every step with our library prep portfolio advancements.

Thumbnail

MiSeq i100 Series: Intro to starting a run

This video walks you step-by-step through planning your run, preparing your samples for sequencing, and setting up the instrument.

Speak to a specialist or attend an event

Looking for more? Reach out to talk to a specialist about the MiSeq i100 Series or explore a variety of events introducing the MiSeq i100 Series, from roadshows in cities around the world to webinars and more.