Illumina library prep and sequencing


Our laboratory provides extensive support for Illumina library preparation, sequencing, and data analysis. We have well-established protocols tailored for common library preparation procedures, and our team is ready to collaborate closely with investigators with specific needs. Whether it's dealing with low input DNA or RNA quantities or custom library preparation protocols, we've got it covered.

You have the option to have your libraries undergo in-house sequencing using our Illumina MiSeq or NextSeq1000. Alternatively, for higher-throughput sequencing, we can prepare libraries for you and then send them off for sequencing elsewhere on a platform like NovaSeq. In such cases, we handle sample submission, manage data delivery logistics, and uphold strict data quality standards.

If you're unsure which Illumina sequencing platform is most suitable for your project, we've prepared a summary comparing sequence outputs (see table below). Additional details are also available on the Illumina website ( Feel free to contact us via email ( for in-depth discussions and clarifications. We're here to assist you in making informed decisions for your research.


Illumina MiSeq and NextSeq descriptions
The Illumina MiSeq sequencing platform is a powerful tool in genomic research. It is compact, flexible, and efficient, making it suitable for various genomic applications. The system can handle projects of different sizes, producing 1 million to 25 million paired-end reads per run. Its adaptability, supporting variable read lengths, makes it ideal for tasks like gene sequencing, amplicon sequencing, small genome sequencing, targeted resequencing, and metagenomics.

One of the MiSeq's strengths is its high accuracy in base calling, ensuring precise results in genomic analyses. The platform's efficient run times, ranging from a few hours to overnight, make it a quick and dependable solution for researchers. The MiSeq employs sequencing-by-synthesis (SBS) chemistry, using 4-channel chemistry with multiple dye combinations to enhance accuracy and efficiency.


Similarly, the Illumina NextSeq instrument also utilizes SBS chemistry to decode millions of DNA fragments simultaneously. It employs a 2-channel chemistry approach with green and red filters, allowing for the capture of two images per cycle. This method facilitates the identification of DNA fragments containing specific bases. The NextSeq systems utilize patterned flow cell technology, nanowells, and lossless genomic compression to increase sequencing reads and total output, providing highly accurate and efficient data for researchers.

2 channel

In summary, both the Illumina MiSeq and NextSeq platforms utilize advanced sequencing technologies, such as SBS chemistry, to deliver precise and flexible genomic sequencing solutions for researchers across various applications.

MiSeq and NextSeq specifications

MiSeq - NextSeq compare


DNA sequencing read counts are guaranteed only for standardized libraries prepared and pooled by the MCIC. However, for new library preparations, a pilot study may be needed to check feasibility, usually at the project’s cost. The number of reads per library—especially in new library preps or unbalanced pools—may not always meet the goals. The information in the table applies mainly to high-diversity genomic DNA samples, and most other applications should expect a 10-20% yield reduction.


Data transfer

Data is released to the user once it has passed our quality checks. All NextSeq and MiSeq run data is shared with the user via BaseSpace. We will store data from all NextSeq and MiSeq runs for three months only. Therefore, we strongly recommend that all users keep a backup of all sequencing data provided by us.

Illumina library preparation services

We offer a variety of Illumina library preparation services, including for:

Following library preparation, these samples can undergo in-house sequencing using our Illumina MiSeqs or NextSeq1000 (common, for instance, in 16S/ITS amplicon sequencing) or be sent to an external facility for sequencing on a higher-throughput sequencer like an Illumina NovaSeq (common, for example, in RNA-seq). 

submitting samples for Illumina library preparation and Sequencing
  1. Read and adhere to the guidelines outlined in the 'Instructions for submitting samples for Illumina Library preparation.
  2. Complete our 'Illumina Library Preparation Sample Submission Form'.
  3. Submit the form through the designated submission webform, including all necessary documents.

Your samples will be added to our queue only upon receiving both the samples and the requested documentation. Typically, the turnaround time for library preparation and sequencing is 4 - 8 weeks, but we can provide a more accurate estimate once you submit your samples.

In-house MiSeq and NextSeq1000 sequencing (Without library prep)

Typical applications for MiSeq and NextSeq sequencing include:

  • 16S/ITS Metagenomics
  • De novo sequencing of small genomes
  • Small RNA Sequencing
  • Highly multiplexed PCR amplicon sequencing
  • Sequencing custom gene panel assays
  • Targeted resequencing

To submit samples for MiSeq and NextSeq1000 sequencing:

  1. Follow the instructions in the 'Instructions for Illumina MiSeq/NextSeq1000 Sequencing Sample Submission' document.
  2. Collect your sample gel images or Bioanalyzer traces. If you need assistance in generating these, feel free to get in touch with us.
  3. Complete the 'Illumina MiSeq/ NextSeq1000 Sequencing Sample Submission Form', and submit it along with the Bioanalyzer traces using our submission webform.

The typical turnaround time for MiSeq or NextSeq sequencing is in the range of 2-4 weeks. For a more accurate estimate, we can provide further details once your samples are in the queue.