How to start using the iSeq 100 System

Prep the lab

Prepare the lab space in advance so that you are ready to install the iSeq 100 System upon delivery. With its small footprint, the iSeq 100 System requires only minimal bench space and an electrical outlet. Use the following guidelines to set up your lab space.

  • Reserve bench space:

    Height 42.5 cm (16.8 in) × Width 30.5 cm (12 in) × Depth 33 cm (13 in)

  • Leave ample space on the left side and behind the instrument so you can access the power switch on the back panel
  • Make sure you can reach the outlet easily with the provided power cord: 2.44 m (8 ft) in North America; 2.5 m (8.2 ft) in all other regions
  • Use the minimum clearance dimensions specified in the site prep guide to make sure the instrument is accessible from all sides


Start exploring how to get the most out of your iSeq 100 System while you wait for it to arrive.

View educational resources about how to use the iSeq 100 System and other common next-generation sequencing topics.

Learn how to get started with the iSeq 100 System and Illumina NGS technology with our free, online training courses.

Considering switching your studies to the iSeq 100 System? See our step-by-step guides to help you transition your current workflows.


Track your iSeq 100 System from shipment to the moment it arrives at the lab. Unpacking and installing the iSeq 100 System takes only ~30 minutes. With convenient carrying handles, the lightweight instrument can be lifted easily and placed on a lab bench.

  • Shipping box weighs 21.8 kg (48 lbs)
  • iSeq 100 System weighs 15.9 kg (35 lbs)
  • Shipping box includes Ethernet cable, power cord, dry test cartridge, and dry test flow cell

Set up

Setting up the iSeq 100 System is as easy as connecting the power cable and turning the system on. Simply follow the onscreen prompts to perform a system check using the reusable test cartridge and flow cell.


During the system check, the iSeq 100 System will guide you through instrument qualification. You can document the results using the following protocols or through an Illumina qualification service.

Independent Qualification

Follow these step-by-step instructions to qualify the instrument independently. To receive a signed Certificate of Qualification, email the completed document to Illumina provides this service one time per calendar year.

Illumina Qualification Service

Need help? Certified Illumina engineers can install and qualify your instrument on site. Our qualification services deliver an audit-ready report to help meet regulatory requirements.


Step-by-step guidance for you and your iSeq 100 System


Choose a library prep kit for your application, whether it’s sequencing microbes, gene panels, or custom content. You can prepare DNA or RNA libraries 1–2 days in advance, according to the manual for your library prep kit.


Starting a sequencing run on an iSeq 100 System takes only a few minutes. Simply load a cartridge and press start. Onscreen prompts will guide you through run setup.


Make sense of your data with Local Run Manager software, installed on every iSeq 100 System. Select the analysis module for your application and the software will automatically perform data analysis.


We’re always here to help. Our training courses can help you get started with library prep, sequencing, and data analysis. Illumina scientists and engineers are available globally to answer questions every step of the way.

Your iSeq 100 System will guide you through how to perform a system check and troubleshoot the instrument. The system is covered by a one-year warranty, which includes a replacement instrument or field service engineer support (depending on region) to minimize downtime.*

*Domestic shipments will arrive in as little as 1–2 days. International shipments may arrive up to 96 hours after ship time. Timing may vary depending on country and instrument condition.

See tips and best practices, online training courses, documentation, and more.
View iSeq 100 system support

Find answers to frequently asked questions about the iSeq 100 System.
Frequently asked questions


iSeq 100 System: Troubleshooting and Support

Focusing on maintenance and run optimization can help ensure maximum uptime and productivity for your iSeq 100 Sequencing System. In this video, we will highlight basic maintenance and troubleshooting activities and resources.


iSeq 100 System: Support Resources

Tim Gilmartin, an Illumina Field Application Scientist, highlights the user guides, video guides, and online courses at your disposal that will help you install and use your iSeq 100 System.