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Illumina MiSeq Run Options

Illumina MiSeq Platform

Illumina MiSeq V2
(2x 250 base PE)1

Illumina MiSeq V2
(2x 150 base PE) 1

Illumina MiSeq V2
(2x 25 base PE) 1

Illumina MiSeq  Micro V2
(2x 150 base PE) 1

Illumina MiSeq  Nano V2
(2x 150 base PE) 1

Illumina MiSeq Nano V2
(2x 250 base  PE) 1

Illumina MiSeq V3
(2x 75 base PE)2

Illumina MiSeq V3

(2x 300 base PE)2

Output

~6-7.5 Gb per run

~3-4.5Gb per run

~750-850Mb per run

~1.0-1.2Gb per run

~250-300Mb per run

~450-500Mb per run

~3-3.8Gb per run

~12-15Gb per run

Number of reads

~24-30 million paired-end reads per run

~24-30 million paired-end reads per run

~24-30 million paired-end reads per run

~ 6.7-8 million paired-end reads per run

~ 1.6-2 million paired-end reads per run

~1.6-2 million paired-end reads per run

~44-50 million paired-end reads per run

~44-50 million paired-end reads per run

MiSeq instrument Data Quality3

75% bases higher than Q30 at 2X250 bp

80% bases higher than Q30 at 2X150 bp

90% bases higher than Q30 at 2X25 bp

80% bases higher than Q30 at 2X150 bp

80% bases higher than Q30 at 2X150 bp

75% bases higher than Q30 at 2X250 bp

85% bases higher than Q30 at 2X75 bp

70% bases higher than Q30 at 2X300 bp

NOTES:

  1.             Version 2 Illumina MiSeq chemistry.
  2.             Version 3 Illumina MiSeq chemistry.
  3.             Illumina Quality Specifications

NOTE: The Illumina Micro and Nano Illumina Miseq kits are suitable for genomic sequencing projects where there are only a small number of small genomes to be sequenced, and also for small scale custom amplicon sequencing projects that require less reads.

Refer to "Sample Preparation, Quantification and Quality Requirements" as a guide for which run lengths are suitable for each application.

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