Best practices for maintaining the computer on Illumina sequencing systems
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Proper maintenance of the instrument computer minimizes computer-related issues during sequencing runs. The following tips help maintain the instrument computer. How often these maintenance steps are recommended is dependent on the usage of the instrument.
Power cycle the computer and instrument
Power cycling resets the instrument computer, memory usage, and software programs. A power cycle consists of shutting down the instrument and computer, leaving the system off for two to five minutes, then restarting the instrument and computer. The instrument contain recommendations for properly power cycling.
Instruments should be left on at all times when not being power cycled to maintain the integrity of the instrument fluidics.
Power cycling the instrument computer regularly can maintain consistent instrument computer performance.
You may be asked to power cycle the instrument during troubleshooting.
The instrument system guides contain recommendations for properly shutting down the instrument and computer for extended periods of time.
Cleaning the hard drives
iSeq 100
Temporary run folders, or “temp folders”, are not deleted by default on the iSeq 100. Without removal, old run folders will reduce hard drive space. The temp folders (D:\Illumina\iSeq Runs) can be managed by deleting the run via Process Management in the control software. Runs in the default output folder on the instrument (D:\SequencingRuns) can only be deleted via the file explorer.
MiniSeq
Temp run folders are not deleted by default on the MiniSeq. Without removal, old run folders will reduce hard drive space. Local Run Manager can be configured for automated deletion of analysis folders, and folder retention time is configured in the Local Run Manager System Settings. Otherwise, run folders require manual deletion.
MiSeq
The hard drive on the MiSeq is configured for processing runs and performing on-instrument analyses and is not meant for long-term storage. Data within the MiSeqTemp folder is automatically cleared after 7 days. It is good practice to move old run folders from the MiSeqAnalysis and MiSeqOutput folders to long-term storage regularly.
NextSeq 500/550
With NextSeq Control Software v2The NextSeq hard drive is designed to store data for one run, which will be automatically overwritten when a new run is started.
With NextSeq Control Software v4The NextSeq hard drive can store multiple runs, but it is recommended to use an output folder in a network location. The data in the temp folder is automatically overwritten when a new run is started. Output folders on the instrument require manual deletion.
HiSeq 1000/2000/1500/2500
HiSeq 3000/4000/X
Quick formatting is the preferred method of data deletion for the output (O:) and scratch (S:) drives. Never format the C:\ and DONOTEJECT drives. Instructions for reformatting can be found in the instrument system guides:
NovaSeq 6000
NovaSeq 6000 temp run folders are not automatically deleted. Without removal, hard drive space can become limited, which can impact data processing. Regularly deleting run folders is recommended. Delete runs from the temp folders via Process Management in the control software.
NextSeq 1000/2000
NextSeq 1000/2000 run folders are not automatically deleted. Without removal, hard drive space can become limited, which can impact data processing. Regularly deleting run folders is recommended. Delete runs from the temp folders via Disk Management in the control software. Deleting runs manually via the file navigation system can negatively impact the control software.
NovaSeq X Plus
Security best practice
It is important that installed antivirus software does not interfere with sequencing runs. For more information, refer to the site prep guide for your system.
Language and Regional settings
Instrument computer language and regional settings are set to English (United States) by default. Do not change this setting. The software is not designed to run in another language. Changing this setting can cause secondary analysis failures and communication problems between the computer and the instrument.
Daylight saving settings are enabled by default for correct syncing with BaseSpace Sequence Hub. Do not change this setting.
HiSeq temp run folders are not automatically deleted. Without removal, hard drive space can become limited, which can impact data processing. Regularly deleting run folders or performing a quick format is recommended. Never reformat the C:\ and DONOTEJECT drives. Instructions for performing a quick format of the HiSeq hard drives can be found in the bulletin.
NovaSeq X Plus run folders are not automatically deleted. If there is insufficient data storage space, a warning notification displays during pre-run checks. Regularly deleting run folders is recommended. See for instructions to delete runs. Deleting runs manually via the file navigation system can negatively impact the control software.
The web page contains recommendations for security configurations on all Illumina sequencing platforms. Further platform-specific recommendations are found in the instrument site prep guides.
For any feedback or questions regarding this article (Illumina Knowledge Article #5253), contact Illumina Technical Support .