Maximum read length for Illumina sequencing platforms

Maximum supported read length

Illumina platforms and sequencing kits allow for a variety of sequencing applications. To ensure the highest level of quality, Illumina supports reads up to a certain length depending on the sequencing platform and SBS kit version; refer to How many cycles of SBS chemistry are in my kit?. It is possible to choose a longer read length during run setup in Local Run Manager (LRM) or the instrument control software. However, when the read length exceeds the supported length Illumina cannot guarantee maintaining high data quality.

Table 1. Maximum supported read length for sequencing platforms and SBS reagent kits.

* MO: Mid-output / HO: High-output ** Rapid Run

Maximum read length for index reads

• Instrument control software: enter custom Index Read length during run setup for certain instruments, as shown below in Table 2.

• LRM v2: enter up to 100 characters for the maximum index cycles (see How to use a custom library prep kit in Local Run Manager v2 for additional information on custom libraries with Local Run Manager).
• LRM v3: enter up to 20 characters, or use manual mode to allow for between 20 and 100 bp.

• LRM v4: enter up to 20 characters, or use manual mode to allow for between 20 and 1000 bp.

• To make sure sequencing quality of the Index Read remains as expected, do not exceed the supported read length.

Table 2. Maximum individual index length for sequencing platforms.

*When setting up runs in Cloud mode, index length is limited to 12 bp.

**For index length between 20-1000 bp, use manual mode as LRM v4 is limited to 20 bp.

***index length is not limited for runs set up in manual mode without analysis

**** Only Supported when using DRAGEN BCL Convert 4.3.13 and up.

Note that BCL Convert has its own index limitations. BCL Convert 4.2 or lower is limited to 27 index cycles total. For BCL Convert 4.3 and higher, the index length has been increased to 27 cycles for each index read.

If using the bclconvert override cycle settings, bases specified for UMIs (U) in the index reads will not count for the maximum index length.

For any feedback or questions regarding this article (Illumina Knowledge Article #2826), contact Illumina Technical Support [e-mail].