Department of Botany & Plant Sciences


Illumina MiSeq DNA Sequencer (operated by Core Staff)

Illumina MiSeq DNA Sequencer



  • This instrument is used by core personnel for sequencing DNA libraries.
  • The MiSeq is a lower throughput sequencer that generate fewer reads (maximum of 25 million reads V3 kits) than the NextSeq but is excellent for applications such as metagenomics studies involved the sequencing of amplicons generated by PCR such as 16s ribosomal DNA.
  • Read lengths range between 50bp single-end to 300bp paired-end (600bp). The instrument provides a variety of useful outputs, including small genome re-sequencing, small genome de novo sequencing and amplicon sequencing for metagenomics studies.
  • A variety of kits are available commercially to users to produce libraries for sequencing including low input kits.
  • Customers can produce their own libraries for sequencing. A common protocol for 16S metagenomics is that offered by Illumina (16s-metagenomic-library-prep-guide-15044223-b) which takes advantage of Nextera dual index barcodes.


  • This instrument if capable of processing a flow cell containing 1 lane but is rapid with run times of 8 hours (50bp single read) to about 48 hours (300bp paired-end read). 
  • The single lane flow cell is capable of generating up to 25 million sequence reads per lane (V3 kit).
  • There is a range of sequencing kit available for the MiSeq including:
    • 50bp single read (up to 15 million reads)
    • 150bp single end/75bp paired end (up to 15 million reads)
    • 300bp single read/150bp paired end (up to 25 million reads)
    • 250bp paired end read (up to 15 million reads)
    • 300bp paired end read (up to 25 million reads)
    • Micro kit 300bp single read/150bp paired end (up to 4 million reads)
    • Nano kit 250bp paired end (up to 1 million reads)
    • Nano kit 300 single read/150 paired-end (up to 1 million reads)
  • Micro and Nano kits are ideal for small-scale or preliminary experiments.
  • Paired-end sequencing permits fragments to be sequenced from both ends, approximately doubling the output of sequence data and aiding in assembly of small genomes such as those of bacteria and fungi.
  • If you have any questions about projects you are considering or the submission process please contact the Genomics Core staff.



For pricing please contact the Genomics Core.


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