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

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Library prep
2
Sequence
3
Analyze

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.

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

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Assay design and library prep
2
Sequence
3
Analyze

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
2
Sequence
3
Analyze

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.

More applications and methods

ChIP-Seq

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

De novo sequencing

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

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.

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.

Targeted DNA sequencing

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

Targeted RNA sequencing

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

How others use this instrument

See what’s possible with the MiSeq System