Specifications for the MiSeq System

MiSeq offers short sequencing run times and long read lengths while maintaining high data quality

MiSeq Specifications

  MiSeq Reagent Kit v2 MiSeq Reagent Kit v3
Read Length 1 × 36 bp 2 × 25 bp 2 × 150 bp 2 × 250 bp 2 × 75 bp 2 × 300 bp
Total Time* ~4 hrs ~5.5 hrs ~24 hrs ~39 hrs ~21 hrs ~56 hrs
Output 540–610 Mb 750–850 Mb 4.5–5.1 Gb 7.5–8.5 Gb 3.3–3.8 Gb 13.2–15 Gb
  MiSeq Reagent Kit v2 Micro MiSeq Reagent Kit v2 Nano
Read Length 2 × 150 bp 2 × 250 bp 2 × 150 bp
Total Time* ~19 hrs ~28 hrs ~17 hrs
Output 1.2 Mb 500 Mb 300 Mb

* Total time includes cluster generation, sequencing, and base calling on a MiSeq System enabled with dual-surface scanning.

  MiSeq Reagent Kit v2 MiSeq Reagent Kit v3 MiSeq Reagent Kit v2 Micro MiSeq Reagent Kit v2 Nano
Single Reads 12–15 million 22–25 million 4 million 1 million
Paired-End Reads 24–30 million 44–50 million 8 million 2 million

** Install specifications based on Illumina PhiX control library at supported cluster densities (865-965 k/mm2 clusters passing filter for v2 chemistry and 1200-1400 k/mm2 clusters passing filter for v3 chemistry). Actual performance parameters may vary based on sample type, sample quality, and clusters passing filter.

MiSeq Reagent Kit v2 MiSeq Reagent Kit v3
> 90% bases higher than Q30 at 1 × 36 bp > 85% bases higher than Q30 at 2 × 75 bp
> 90% bases higher than Q30 at 2 × 25 bp > 70% bases higher than Q30 at 2 × 300 bp
> 80% bases higher than Q30 at 2 × 150 bp  
> 75% bases higher than Q30 at 2 × 250 bp  

† A quality score (Q-score) is a prediction of the probability of an error in base calling. The percentage of bases > Q30 is averaged across the entire run.

MiSeq System Specification Sheet

MiSeq System Specification Sheet

The MiSeq System offers a DNA-to-results sequencing solution with a small footprint that fits into virtually any lab environment.

View Specification Sheet
Sequencing by Synthesis (SBS) Technology

The MiSeq System harnesses proven Illumina SBS technology to deliver highly accurate data and robust performance for a broad range of applications. SBS uses a reversible-terminator method, with fluorescently labeled nucleotides to detect single bases as they are incorporated into growing DNA strands.

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Paired-End Sequencing Technology

Paired-end sequencing enables both ends of the DNA fragment to be sequenced. Because the distance between each paired read is known, alignment algorithms can use this information to map the reads. This is especially helpful across difficult-to-sequence, repetitive regions of the genome.

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