Instruments

MiniSeq Sequencing System applications and methods

Accessible cross-method flexibility

Transition easily between sequencing methods for DNA and RNA applications

MiniSeq flow cell

Key applications and methods

Targeted DNA sequencing allows researchers to focus on a select set of genes or relevant gene regions using fixed panels of expert-selected content or custom, user-defined gene panels. By focusing the power of next-generation sequencing (NGS), targeted sequencing enables cost-effective and systematic variant detection with high accuracy and reproducibility.  

Read respiratory pathogen application note

1
Design assay and 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

MiniSeq Reagent Kit

Ready-to-use reagent kits include the reagent cartridge, flow cell, and hybridization buffer for use with the MiniSeq 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 targeted DNA sequencing education

The MiniSeq System sequences up to 50 small genomes per run* to provide a detailed view of the genomes of the smallest organisms. 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.

1
Prep

Nextera XT DNA Library Prep 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

MiniSeq Reagent Kit

Ready-to-use reagent kits include the reagent cartridge, flow cell, and hybridization buffer for use with the MiniSeq System.

3
Analyze

Local Run Manager

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

TELL-Seq Data Analysis Pipeline

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

Whole-Genome Sequencing app

Rapid alignment, variant calling, and annotation tool to quickly extract biological information from whole-genome sequences.

Find small WGS education

*Based on 5 Mb genome, 30× coverage, 2 × 150 bp read length, Nextera XT Library Prep Kit, and MiniSeq Reagent High Output 300-cycle kit.

Targeted RNA sequencing (RNA-Seq) using the MiniSeq System enables gene expression measurement of dozens to thousands of targets simultaneously.† The MiniSeq System supports user-defined panels to target genes, isoforms, splice junctions, cSNPs, and fusion genes. Predefined panels of expert-selected content target major signal transduction pathways and cellular processes. Sequence 1–384 targeted RNA samples per run.

1
Design assay and prep

AmpliSeq for Illumina Custom RNA Panel

Targeted, custom RNA research panels optimized for sequencing up to 1200 genomic targets of interest.

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

MiniSeq Reagent Kit

Ready-to-use reagent kits include the reagent cartridge, flow cell, and hybridization buffer for use with the MiniSeq System.

3
Analyze

TruSeq Targeted RNA

A tool to analyze RNA samples that have been prepared using TruSeq RNA Expression Kits with sample MiniSeq Targeted RNA data available.

Find targeted RNA-Seq education

†Based on 65 targets, 1000× coverage, 1 × 50 bp read length, TruSeq Targeted RNA Expression custom panel kit, and MiniSeq Reagent High Output 75-cycle kit.

Resource spotlight

Bring bioinformatics in-house to cut costs and time

Learn how the MiniSeq System coupled with other Illumina solutions enabled Phosphorus to perform genomic analysis onsite at an accessible price point.

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More applications and methods

16S metagenomic sequencing

Sequence the 16S ribosomal RNA (rRNA) gene with a culture-free method to identify and compare bacteria from complex, difficult-to-study microbiomes or environments.

Learn more about 16S rRNA sequencing
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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Genotyping by sequencing (GBS)

Discover novel plant and animal SNPs and perform genotyping studies with a low-cost genetic screening method.

Learn more about GBS
Germline mutation analysis

Assess genes with known or suspected associations with an increased hereditary risk of cancer.

Learn more about germline mutation studies
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Pathogen identification and analysis

Leverage NGS to detect and characterize viruses, bacteria, fungi, and parasites for research applications.

Learn more about pathogen identification
Read respiratory virus application note
Read respiratory pathogen application note
Small RNA discovery and profiling

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-Seq
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Targeted gene sequencing

Select and sequence specific genes or genomic regions of interest using predesigned or custom designed panels for gene profiling studies.

Learn more about targeted gene sequencing

How others use this instrument

See what’s possible with the MiniSeq System