MiSeq Applications & Methods
Key Applications and Methods
Get a detailed genome view of the smallest organisms. Small genome sequencing provides comprehensive analysis of microbial or viral genomes for public health, epidemiology, and disease studies. Sequence up to 24 small genomes per MiSeq run.
See how other researchers are using small genome sequencing on the MiSeq System for microbial genomics studies:
Library Prep
90 mins/15 mins hands-on
Nextera XT Library Prep Kit
Prepare sequencing libraries for small genomes, PCR amplicons, and plasmids in less than 90 min, with a low DNA input requirement.
Illumina DNA Prep
A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.
Sequence
56 hours/15 mins hands-on
MiSeq Reagent Kit v3 600 cycles
Optimized chemistry to increase cluster density and read length, and improve sequencing quality scores, compared to earlier kit versions.
Analyze
3 hours
SPAdes Genome Assembler
Open source tool for de novo sequencing, designed to assemble small genomes from MDA single-cell and standard bacterial data sets.
TELLSeq App
Tell-Read and Tell-Link App links reads and creates assemblies for de novo WGS.
Browse sample data in Basespace Sequence Hub (login required):
MiSeq Small Genome Data
Estimated Cost Per Sample: $98*
*Small whole-genome sequencing on the MiSeq System estimated cost per sample calculated 2016, based on 5 Mb genome, 50-100X coverage, 2 x 300 bp read length, Nextera XT Library Prep Kit, MiSeq Reagent v3 600-cycle kit
Targeted resequencing focuses time, expenses, and analysis on sequencing only a subset of genes or genome regions of research interest. Amplicon sequencing, the ultra-deep 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 run.
Assay Design & Library Prep
5-7 hours
AmpliSeq for Illumina Sequencing Solution
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 Software
Sequence
17-32 hours
MiSeq Reagent Kit v2 (300 cycles)
MiSeq sequencing reagents in pre-filled, ready-to-use cartridges. Micro and nano formats are available for low output applications.
Data Analysis
3 hours
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.
BaseSpace Variant Interpreter
Enables researchers to rapidly identify biologically significant variants from human genomic data.
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. Our demonstrated protocol for 16S rRNA sequencing can help take the guess work out of your experiments. Multiplexing lets you sequence up to 96 samples per MiSeq run.
See how other researchers are using the MiSeq System to power their metagenomics studies:
Library Prep
3 hours/30 mins hands-on
Nextera XT Index Kit v2
Nextera XT index kits allow for up to 384 uniquely indexed samples to be pooled and sequenced on a single sequencing run.
Sequence
56 hours/15 mins hands-on
MiSeq Reagent Kit v3 (600 cycles)
Optimized chemistry to increase cluster density and read length, and improve sequencing quality scores, compared to earlier kit versions.
Analyze
3 hours
16S Metagenomics BaseSpace App
Performs taxonomic classification of 16S rRNA targeted amplicon reads using an Illumina-curated version of the GreenGenes taxonomic database.
Browse sample data in BaseSpace Sequence Hub (login required):
16S Metagenomic Sequencing Run
16S Metagenomic Sequencing Project
Estimated Cost Per Sample: $18*
*16S rRNA sequencing on the MiSeq System estimated cost per sample calculated 2016, based on 96 samples, 2 x 300 bp read length, Nextera XT index primers, MiSeq Reagent v3 600-cycle kit
NGS is Fueling Species Research in Australia
High-throughput sequencing is paving the way to support agriculture, aquaculture, biodiversity, and conservation studies at the Deakin Genomics Center
Read InterviewMore Applications and Methods
Gene Expression Analysis with Targeted RNA-Seq
Targeted RNA sequencing (RNA-Seq) focuses on specific transcripts of interest, used to analyze gene expression and identify fusion genes.
Application Note
TruSeq Targeted RNA Expression Solution for the MiSeq System
Researcher Interviews
Cancer Pathways in Pediatric Leukemia
Uncovering Effect of CNV Linked to Schizophrenia
Targeted Gene Panels
Targeted gene sequencing panels contain defined probe sets focused on specific genes of interest. Both predesigned and custom panels are available.
Researcher Interviews
Seeking Out Dyslipidemia Variants with LipidSeq
NGS Proves Invaluable for Biomarker Discovery
De Novo Sequencing
De novo sequencing with next-generation sequencing (NGS) enables fast, accurate characterization of species without a reference genome.
Application Note
TELLSeq: Bringing Speed and Accuracy to Long-Range Sequencing
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.
DNA-Protein Interaction Analysis with ChIP-Seq
Combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP-Seq is a powerful method for genome-wide surveys of gene regulation.
Researcher Interview
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.
Researcher Interview
Methods Guide
Access the information you need—from BeadChip arrays to library preparation for genome, transcriptome, or epigenome studies to sequencer selection, analysis, and support—all in one place. Select the best tools for your lab with our comprehensive guide designed specifically for research applications.
Access Guide