MiSeq

MiSeq is a benchtop next-generation sequencing instrument developed by Illumina, designed for small-scale sequencing projects, targeted panels, and microbial genomics. Introduced in 2011, the MiSeq uses Illumina's sequencing-by-synthesis (SBS) chemistry with reversible terminators. It combines a compact instrument body, integrated flow cell, optics, and fluidics for automated cycles of nucleotide incorporation on a flow cell, enabling parallel sequencing of many DNA fragments.

The platform supports paired-end sequencing with read lengths up to 2x300 bases using specific reagent kits; common configurations include 2x150 and 2x250 reads. Throughput is modest compared with larger Illumina systems and varies by kit and read length, ranging from hundreds of megabases to a few gigabases per run. Typical run times are on the order of several hours.

Data produced are base-called reads which, after demultiplexing, are delivered as FASTQ files suitable for downstream analyses. Runs are configured and monitored with MiSeq Control Software (MCS) on the instrument, and the system can perform onboard data processing and basic quality checks.

Applications include amplicon sequencing (such as 16S rRNA gene profiling), targeted gene panels, small genome sequencing, plasmid verification, and quality control in clinical and research settings. While not intended for large-scale whole-genome projects, MiSeq remains a popular choice for focused sequencing tasks that require rapid turnaround and a compact footprint.