Miseq (Illumina) is a new generation of miniaturized sequencing instrument (bench-top) launched on February 2011, which uses a chemical method based on Illumina TruSeq technology that nucleotide sequencing-by-synthesis by reversible terminator. Compared with Hiseq2000, the unparalleled accuracy of next-generation sequencing reagents, transitory sequencing time by   new fluid system are the main advantages, although the throughput of a run is low.


Performance Parameters

Read Length

Run Time




About 24 hours




About 39 hours




(1)The above performance is based on Miseq sequencing V2 reagent. V1 reagent only supports 2x150bp, runs about 27 hours, 1.5-2Gb throughput, Q30>80%. But V1 reagent is no longer ordered.

(2)This data is based on Illumina control libraries PhiX (a balanced representation of A, T, G, and C nucleotides). The appropriate clusters density is 900-1200K/mm2, and 880-965K/mm2 after PF. But different sample sequencing results by their own properties.


Technical Features

1.    Short sequencing cycle: Miseq V2 150PE is short to 24 hours running time, so it can used for fast and efficient amplicon sequencing and small genome sequencing, with a small amount of time to complete projects of small amount of data.

2.    Up to 250bp of paired-end read-length:Miseq sequencing read length has reached 2x250bp, which can effectively across complex genomes highly repetitive regions,thereby enhancing the effect of assembly, more conducive for gene annotation and gene function dig.

3.    Convenient sequencing process: Miseq is a compact, integrated platform for integration of cluster generation, Pair-end sequencing and complete data analysis, saving laboratory space. Through an intuitive touch-screen interface to carry out simple instrument operation, plug and play reagent with RFID tracking, with automated convenience.


Sequencing Process


1.Amplicon sequencing

Long read-length capability of paired-end, speed and high data quality, so ampilicon sequencing project can be completed within a few days.

2.Transcriptome sequencing

Compared with the 454 sequencer, similar length,cheap,easy to implement de novo assembly, more comprehensive gene annotation.

3.Small genomes De novo assembly

2x250bp read length and high-throughput up to 7G are suitable as the project for small genome such microbes because of mosaic effect.

4.Microbial diversity analysis

2x250bp read length can measured through some of the variable region, more conducive to improving the accuracy of analytical results.