Instruments

MiSeq Sequencing System applications and methods

Explore the possibilities

The MiSeq System delivers flexibility and simplicity for a broad range of applications, including targeted gene and small-genome sequencing

MiSeq flow cell

Key applications and methods

Small whole-genome sequencing (WGS) enables comprehensive analysis of microbial or viral genomes for applications in public health, infectious disease surveillance, molecular epidemiology studies, and environmental metagenomics. This approach does not require bacterial culture or labor-intensive cloning steps. Sequence up to 24 small genomes per MiSeq System sequencing run.

Read application note: microbial WGS

Read customer interview: epidemiology research

1
Library prep

Nextera XT DNA Library Preparation Kit

Rapid library prep optimized for small genomes, PCR amplicons, and plasmids, requiring as little as 1 ng of input and 15 minutes of hands-on-time.

Illumina DNA Prep

Fast, integrated workflow for a wide range of applications, including sequencing of whole human genomes, amplicons, plasmids, and microbial genomes.

2
Sequence

MiSeq Reagent Kit v3 (600 cycles)

Pre-filled, ready-to-use cartridges containing clustering and sequencing reagents to support a 600-cycle run on the MiSeq System.

3
Analyze

SPAdes Genome Assembler app

Open-source tool for de novo assembly of small genomes from MDA single-cell and standard bacterial data sets from next-generation sequencing data.

TELL-Seq Data Analysis Pipeline app

Two data analysis pipelines (Tell-Read and Tell-Link) for microbial genome assembly.

Browse sample data in BaseSpace Sequence Hub (login required): MiSeq small genome data

Estimated cost per sample: $80*

*Small whole-genome sequencing on the MiSeq System estimated cost per sample calculated 2016, based on 5 Mb genome, 50–100× coverage, 2 × 300 bp read length, Nextera XT Library Prep Kit, MiSeq Reagent v3 600-cycle kit.

Find small WGS education

Targeted gene sequencing focuses time, expenses, and analysis on sequencing only genes or genome regions of interest. Amplicon sequencing, the ultradeep targeted sequencing of PCR amplicons, enables cost-effective analysis of up to hundreds of target genomic regions in one assay. Sequence up to 96 samples and 1536 amplicons or more in a single MiSeq System sequencing run.

Read customer interview: bacterial drug resistance

1
Assay design and library prep

AmpliSeq for Illumina

A highly multiplexed polymerase chain reaction (PCR)–based workflow for use with targets ranging from a few to hundreds of genes in a single run.

DesignStudio Assay Design Tool

A web-based assay design tool to help researchers design and order custom sequencing probes or create custom genotyping array assays.

2
Sequence

MiSeq Reagent Kit v2 (300 cycles)

Prefilled, ready-to-use cartridges containing clustering and sequencing reagents to support a 300-cycle run on the MiSeq System.

3
Analyze

Local Run Manager

An on-premises software solution for creating sequencing runs, monitoring run status, and analyzing data.

BaseSpace Sequence Hub

The Illumina genomics cloud-computing environment for NGS data analysis and management.

Find amplicon sequencing education

Sequencing the 16S ribosomal RNA (rRNA) gene is a culture-free method to identify and compare bacteria from complex microbiomes or environments that are difficult to study. The Illumina demonstrated protocol for 16S rRNA sequencing can help take the guesswork out of experiments. Multiplexing lets you sequence up to 96 samples per MiSeq System sequencing run.

Read application note: 16S metagenomics studies

Read customer interview: microbial community studies

1
Library prep

Nextera XT Index Kit v2

Indexes for pooling and sequencing up to 384 uniquely indexed samples on a single sequencing run.

16S metagenomic sequencing protocol

A comprehensive workflow using the MiSeq System for 16S rRNA amplicon sequencing.

2
Sequence

MiSeq Reagent Kit v3 (600 cycles)

Pre-filled, ready-to-use cartridges containing clustering and sequencing reagents to support a 600-cycle run on the MiSeq System.

3
Analyze

16S Metagenomics app

Taxonomic classification of 16S rRNA targeted amplicon reads using a version of the GreenGenes taxonomic database curated by Illumina.

Browse sample data in BaseSpace Sequence Hub (login required):

16S metagenomic sequencing run

16S metagenomic sequencing project

Estimated cost per sample: $10* 

*16S rRNA sequencing on the MiSeq System estimated cost per sample calculated 2016, based on 96 samples, 2 × 300 bp read length, Nextera XT index primers, MiSeq Reagent v3 600-cycle kit.

Find 16S rRNA sequencing education

Resource Spotlight

MiSeq self-service resources: Your MiSeq companion

The MiSeq System self-service booklet is an interactive guide that includes clickable features accessible on your computer, tablet, and smartphone. Explore run preparation, instrument maintenance, troubleshooting, and much more. View video: MiSeq self-service booklet intro

View interactive guide

More applications and methods

ChIP-Seq

Analyze protein interactions with DNA for genome-wide surveys of gene regulation.

Learn more about ChIP-Seq
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De novo sequencing

Enable fast, accurate characterization of novel genomes with no reference sequence available for any species.

Learn more about de novo sequencing
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miRNA & small RNA analysis

Isolate and sequence small RNA species, such as microRNA, to study the role of noncoding RNA in gene silencing and posttranscriptional regulation.

Learn more about small RNA analysis
Quality control

Perform quality control (QC) applications for bioproduction studies or assess the quality of a sequencing library before committing it to a full-scale run.

Read QC application note
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Targeted DNA sequencing

Focus time, expenses, and analysis on sequencing only genes or genome regions of interest.

Learn more about targeted DNA sequencing
Read customer interview
Targeted RNA sequencing

Select and sequence specific transcripts of interest for gene expression profiling studies.

Learn more about targeted RNA-Seq
Read application note
Read customer interview

How others use this instrument

See what’s possible with the MiSeq System