Illumina Miseq

The Miseq is our budget friendly benchtop sequencing system, which is typically used when a relatively small output is needed ex. Amplicon sequencing or whole genome sequencing of small genomes (Bacteria, virus etc.). Several different Sequencing kits are available for the Miseq covering a wide range of outputs, read lengths and prices.

Specifications

Sequencing output per flow cell & runtimes

Miseq Reagent kit v2 Miseq Reagent kit v3
Read length 1 x 36 bp 2 x 25 bp 2 x 150 bp 2 x 250 bp 2 x 75 bp 2 x 300 bp
Total Time 4 hours 5,5 hours 24 hours 39 hours 21 hours 56 hours
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

Mb= Mega bases, Gb= Giga bases

Miseq Reagent Kit v2 Micro Miseq Reagent kit v2 Nano
Read Length 2 x 150 bp 2 x 250 bp 2 x 150 bp
Total Time 19 hours 28 hours 17 hours
Output 1,2 Gb 500 Mb 300 Mb

Mb= Mega bases, Gb= Giga bases

The outputs listed in the table above, should only be used as a guideline. As the final output of a sequencing run depends on the given sequencing library.

Reads passing QC filter per Flow cell

Miseq Reagent kit v2 Miseq Reagent kit v3 Miseq Reagent Kit v2 Micro Miseq Reagent kit v2 Nano
Single-end Reads 12-15 million 22-25 million 4 million 1 million
Paired-end Reads 24-30 million 44-55 million 8 million 2 million

 

Quality Scores

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

The Q-Score predicts the probability of an error in the base calling. A Q-score of 30 is equal to a base call accuracy of 99, 9% or in other words an incorrect base call for 1 in a 1000 bases.