Maximum read lengths and number of cycles for different NextSeq 500/550 kits
Maximum supported read length
Illumina platforms and sequencing kits allow for a variety of sequencing applications.
To achieve the highest level of quality, Illumina supports reads up to a certain length depending on the sequencing platform and SBS kit version.
It is possible to choose a longer read length during run setup in Local Run Manager (LRM) or the instrument control software.
When the read length exceeds the supported length Illumina cannot guarantee maintaining high data quality.
Maximum read length for NextSeq 500/550 runs
SBS Kit Version | Maximum Read Length |
Mid-Output | 2 x 151 bp |
High-Output | 2 x 151 bp |
Maximum read lengths for index reads for NextSeq 500/550 runs
Instrument control software
Enter custom Index Read length during run setup as shown in the table below.
LRM v2
Enter up to 100 characters maximum for the index cycles. - For further information, search for Knowledge Base article Local Run Manager 2 - How to use a custom library prep kit.
LRM v3
Enter up to 20 characters maximum for the index cycles or use manual mode if the required length is between 20 and 100 bp.
For the highest sequencing quality of the Index Read, do not exceed the supported read length.
NextSeq Control Software (NCS) version | Single or Dual Index (Maximum Length) |
NCS v2 | 20 bp |
NCS v4 | 20 bp |
Number of guaranteed cycles of SBS chemistry in each kit type for the NextSeq 500/550
Making sure that sufficient volumes of SBS reagents are loaded onto the sequencing instrument is crucial for a successful run.
Running out of reagents during a run impacts intensity and quality, and can result in a run failure.
Dual-index sequencing, depending on the instrument, follows different workflows as shown in the Indexed Sequencing Overview Guide.
The following table outlines available reagent kit sizes and the maximum number of cycles each kit can perform on the NextSeq 500/550.
Reagent Type | Reagent Kit Size | Maximum Number of Cycles | Additional Cycles Needed for Dual Index? |
HO or MO | 75 | 92 | No |
HO or MO | 150 | 168 | No |
HO or MO | 300 | 318 | No |
HO = High-output, MO = Mid-output
For information regarding other Illumina sequencing platforms, search for Knowledge Base articles Maximum read length for Illumina sequencing platforms and How many cycles of SBS chemistry are in my kit?
For any feedback or questions regarding this article (Illumina Knowledge Article #7448), contact Illumina Technical Support techsupport@illumina.com. |
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