Instruments

MiSeq Sequencing System specifications

High performance made simple

Short run times, adjustable read lengths, and multiple flow cell options in one compact benchtop sequencing system

MiSeq system render

Output per flow cell for various read lengthsa,b

MiSeq Sequencing System

Read length MiSeq Reagent Nano Kit v2 MiSeq Reagent Micro Kit v2 MiSeq Reagent Kit v2 MiSeq Reagent Kit v3
1 × 36 bp N/A N/A 540–610 Mb N/A
2 × 25 bp N/A N/A 750–850 Mb N/A
2 × 75 bp N/A N/A N/A 3.3–3.8 Gb
2 × 150 bp 300 Mb 1.2 Gb 4.5–5.1 Gb N/A
2 × 250 bp 500 Mb N/A 7.5–8.5 Gb N/A
2 × 300 bp N/A N/A N/A 13.2–15 Gb

a. The MiSeq System runs a single flow cell. Output per flow cell and output per run are the same. 

b. Specifications based on Illumina PhiX control library at supported cluster densities.

Reads passing filter per flow cella

MiSeq Sequencing System

  MiSeq Reagent Nano Kit v2 MiSeq Reagent Micro Kit v2 MiSeq Reagent Kit v2 MiSeq Reagent Kit v3
Single-end reads 1M 4M 12–15M 22–25M
Paired-end reads 2M 8M 24–30M 44–50M

a. Install specifications based on Illumina PhiX control library at supported cluster densities between 467–583 k/mm2 clusters passing filter for v2 chemistry and 727–827 k/mm2 clusters passing filter for v3 chemistry. Actual performance parameters may vary based on library type, library quality, and clusters passing filter.

Quality scoresa

MiSeq Sequencing System

Read length MiSeq Reagent Nano Kit v2 MiSeq Reagent Micro Kit v2 MiSeq Reagent Kit v2 MiSeq Reagent Kit v3
2 × 25 bp N/A N/A > 90% bases higher than Q30 N/A
2 × 75 bp N/A N/A N/A > 85% bases higher than Q30
2 × 150 bp N/A N/A > 80% bases higher than Q30 N/A
2 × 250 bp N/A N/A > 75% bases higher than Q30 N/A
2 × 300 bp N/A N/A N/A > 70% bases higher than Q30

a. The percentage of bases > Q30 is averaged across the entire run.

Run timea

MiSeq Sequencing System

Read length MiSeq Reagent Nano Kit v2 MiSeq Reagent Micro Kit v2 MiSeq Reagent Kit v2 MiSeq Reagent Kit v3
2 × 25 bp N/A N/A ~5.5 hr N/A
2 × 75 bp N/A N/A N/A ~21 hr
2 × 150 bp ~17 hr ~19 hr ~24 hr N/A
2 × 250 bp ~28 hr N/A ~39 hr N/A
2 × 300 bp N/A N/A N/A ~56 hr

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

Instrument specifications

MiSeq system specifications

MiSeq instrument specifications

  • Light emitting diode (LED)
    Wavelengths
    520 nm, 660 nm
  • Dimensions
    W x D x H
    68.6 cm × 56.5 cm × 52.3 cm
    (27.0 in × 22.2 in × 20.6 in)
  • Dry weight
    57.2 kg (126 lb)
  • Crated weight
    93.6 kg (206 lb)
View in-depth specs sheet (PDF)

Key technologies

Sequencing by synthesis chemistry

The MiSeq System leverages proven Illumina sequencing by synthesis (SBS) chemistry to deliver accurate data and robust performance. SBS chemistry uses reversible-terminator fluorescently labeled nucleotides to detect single bases as they are incorporated into growing DNA strands, reading billions of sequences in parallel.

Paired-end sequencing

The MiSeq System incorporates paired-end sequencing that 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.