iSeq 100 FAQs

The iSeq 100 System contains no field-adjustable parts, so you can install it without Illumina personnel. For instructions, see the  iSeq 100 Sequencing System Setup Poster (document # 1000000035963).

The iSeq 100 flow cell can generate 1.2 Gb per sequencing run. For detailed performance parameters, see Specifications for the iSeq 100 Sequencing System.

The reusable test cartridge and reusable test flow cell that shipped with the instrument are for performing system checks. A system check is performed after hardware installation to confirm proper function, and again as needed for troubleshooting.

The test cartridge and flow cell are reusable components that do not contain reagents or other chemistry. For sequencing, use the single-use reagent cartridge and flow cell provided in iSeq 100 i1 Reagents.

The iSeq 100 System has no serviceable parts. Instead, the Illumina Community and support website provide an online forum for comprehensive support and troubleshooting guidance. Onboard system diagnostics can identify hardware failures that Illumina Technical Support can confirm. Other failures are related to library preparation or consumables.

In the unlikely event than a nonrecoverable hardware failure occurs, Technical Support initiates an exchange and Illumina replaces the system through a process called advanced exchange. Steps to return the instrument include clearing data, decontamination, and return shipping.

For more troubleshooting guidance and advanced exchange information, see the  iSeq 100 Sequencing System Guide (document # 1000000036024).

Advanced Exchange is a process that replaces a damaged or defective system with a refurbished system:

1. Illumina Technical Support determines the best resolution for an issue is Advanced Exchange.
2. Illumina sends a replacement iSeq 100 System.
3. Complete the electronic DCIR form sent by Illumina Technical Support.
4. Package the defective system.
5. Schedule a pickup to ship the defective system back to Illumina.

For detailed information and instructions, see the iSeq 100 Sequencing System Guide (document # 1000000036024).

The iSeq 100 System is designed for small genome and amplicon sequencing with associated analysis options (BaseSpace Apps or Local Run Manager modules). However, many other applications are compatible. Public data sets are available in BaseSpace Sequence Hub.

The iSeq Control Software is integrated with Local Run Manager, where you can directly input sample information or import a legacy sample sheet.

The number of libraries you can sequence at one time depends on the desired coverage for 4 million reads. Using supported Illumina kits, you can multiplex up to 384 libraries. For coverage considerations, see the Sequencing Coverage Calculator.

Libraries loaded onto the iSeq 100 System must be dual-stranded DNA. Skip bead-based normalization included as an option in the following Illumina library prep protocols and instead manually normalize libraries. The bead-based normalization procedure generates single-stranded libraries.

• Nextera XT DNA
• TruSeq Amplicon Cancer Panel
• TruSeq Bovine Parentage Sequencing Panel
• TruSeq Custom Amplicon v1.5
• TruSeq Custom Amplicon Low Input
• TruSight Myeloid
• TruSight Tumor 170

For information on normalization methods, see Library quantification and quality control quick reference guide.

The iSeq 100 System loading volume is 20 µl at a concentration of 50, 60, 100, or 200 pM, depending on library type. Before the run, libraries are diluted to the loading concentration and loaded into the cartridge. Libraries are automatically transferred to the flow cell after the run starts and denatured onboard the instrument.

For details and instructions on diluting libraries, see the  iSeq 100 Sequencing System Guide (document # 1000000036024).

Yes, iSeq 100 i1 Reagents include all consumables to support both single-read and paired-end sequencing. During run setup, you can configure the run to generate either single-read or paired-end data.

No. The iSeq 100 System and consumables are not designed for custom primers.

The iSeq 100 System supports read lengths up to 2 x 151 bp.

The 300-cycle reagents support up to 322 cycles of sequencing to allow for dual 10 bp indexes on a 2 × 151 run.

No. Reagents and libraries stay contained within the disposable cartridge during the run. Therefore, the instrument has no washable parts.

The control software displays standard run metrics onscreen during the run. For more detailed metrics, use a supported version of Sequencing Analysis Viewer (SAV).

You can download SAV for use on a computer or use BaseSpace Sequence Hub. For more information on SAV, see the Sequencing Analysis Viewer Software Guide (document # 15066069).

Local Run Manager is the preferred analysis solution for the iSeq 100 System because it simplifies the end-to-end workflow. You enter all sample information into Local Run Manager and it is automatically sent to the control software. After the run is complete, you can analyze the data locally in Local Run Manager, copy files to BaseSpace Sequence Hub for analysis, or both.

Using BaseSpace Sequence Hub independently of Local Run Manager is also an analysis option. For third-party and user-developed analysis packages, you can use the bcl2fastq2 converter.

Use bcl2fastq2 Conversion Software v2.20, or later, to process data from the iSeq 100 System.

Yes. The local instrument storage can store data until the local storage limit is reached, so starting runs with ample free space is recommended. The analysis and data transfer software continue processing and resume data transfer when the network is restored.