Questions & Answers

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How is the iSeq 100 System installed?

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).

What is the throughput of the iSeq 100 System?

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.

What is the reusable test cartridge? What is the reusable test flow cell?

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.

Will the iSeq 100 System be serviced by Illumina personnel?

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).


Which applications can I run on the iSeq 100 System?

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.

Where do I input my sample information?

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

How many libraries can I sequence on the iSeq 100 System at one time on?

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.

What is the recommended normalization method?

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.

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

What is the iSeq 100 System loading concentration and volume?

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).

Reagents and Flow Cells

Does the iSeq 100 System support paired-end sequencing?

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.

Can I use custom primers on the iSeq 100 System?

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


What is the maximum read length for a sequencing run?

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

How many cycles does iSeq 100 i1 Reagents support?

The 300-cycle reagents support up to 318 cycles of sequencing to allow for dual 8 bp indexes on a 2 x 151 run.

Do I need to wash my iSeq 100 System?

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


Can I use Sequencing Analysis Viewer to view data from an iSeq 100run?

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).


What are my options for analyzing iSeq 100 sequencing data?

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.

What version of bcl2fastq is supported for the iSeq 100 System?

Any supported version of the bcl2fastq Conversion Software can process iSeq 100 System data.

If a network outage occurs, can the iSeq 100 System cache an entire 2 x 150 run?

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.