Transition Notice: Retirement of Legacy Illumina MiSeq Systems

Following our recent announcement regarding the addition of the Illumina MiSeq i100 to our fleet, we are now providing formal notice regarding the decommissioning of our legacy MiSeq instruments.

After more than 10 years of reliable service, our original MiSeq systems are reaching the end of their operational lifecycle. To maintain the highest standards of sequencing efficiency and data quality, we will be decommissioning these instruments sometime before the end of this year (specific date TBD).

The MiSeq i100 utilises 2-color XLEAP-SBS chemistry, ExAmp clustering, and patterned flow cells. This is a significant shift from the 4-color chemistry and bridge amplification used by the older units. We are highlighting this transition now to ensure you have ample time to prepare.

If your current research is strictly dependent on the legacy MiSeq platform, please take note that if you are in the middle of a long-term longitudinal study, we recommend conducting any necessary cross-platform validation or “bridging” runs immediately while both systems remain online.

Why the transition is necessary

While the legacy MiSeq has been a workhorse for a decade, the shift to the i100 architecture — which mirrors the technology found in the NovaSeq X and NextSeq 2000 — allows us to provide faster turnaround times and better data quality at a lower price. Maintaining the older 4-color systems is no longer sustainable as we modernise our laboratory to these newer standards.

Read more about the new MiSeq i100 here.

Support

Our coordinator team is available to discuss how these chemistry changes (4-color vs. 2-color) may affect your analysis pipelines or library preparation kits. We are committed to ensuring that your transition to the i100 is seamless and that your data remains consistent.

Last Updated: 23rd January 2026