Does My HiSeq Need a Tune-UP?

Check these 5 things.

illumina_hiseq2500.jpgWe don’t need to tell you the importance of having your HiSeq operating at its full potential, but it can be difficult to determine if your machine is in need of a preventative maintenance visit.

But luckily there are a few tell-tale signs to look for in each area. If you feel that your HiSeq performance is beginning to decline, and you’re noticing discrepancies in your data, check for these 5 things for common errors.


There are plenty of signs to look for when you’re examining your data. If you notice swath, tile, or lane dropouts, low clusters passing through the filter, or blurry thumbnail images, it could be time to schedule a maintenance visit. Other signals that may mean you need to call the experts are auto-tilt failures, Z-height errors, focus errors, and Q30 drop late in runs.


Fluidics make up an important part of HiSeq machines. Common errors you may notice include low wash volume, no flow from one or more lanes, and sticky vacuum levers. We’ve also had reports of sipper handles being difficult to move up and down and flow cell or chiller door open messages. If you’ve seen any of these errors, it’s time to schedule your PM visit.

Flow Cell Holder

One of the parts we commonly see issues with is the flow cell holder. Often, the flow cell will not seat properly, the vacuum switch won’t turn green quickly or will stay orange, or will require multiple cleanings. These errors could be signs of a bigger issue, so have an expert to take a look at this part.


In addition to optimizing laser alignment, SeqGen’s HiSeq PM will optimize flow cell temperature and monitor chiller temperature. Our service technicians are also trained to check and clean the fluidics system and check the cooling system for leaks and coolant level. SeqGen’s engineers ensure that all subsystems on the HiSeq are within Illumina standards at the completion of each PM visit.


The most common issues we see with the computer are communication problems. Sometimes, the HiSeq Control Software will not connect with the computer, RTA takes longer than normal after a run completion or your computer is simply taking a long time to respond to commands. These can all seem like minor issues, but they can turn into major problems if not address with a routine preventative maintenance visit.

These are just some of the most common signals that indicate you need to call SeqGen to schedule a PM visit on your HiSeq machine. While we don’t have enough space to list every single issue, you’re more than welcome to ask us about a particular issue you’re having.  We’re always happy to help a friend!


Written by Susan Henry

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