SP500 useable read lengths

Question

[noodle]

Hi all,

Can someone share what the usable read lengths are for the 'NovaSeq 6000 SP Reagent Kit v1.5 (500 cycles)'?

For example, the SP100 kit is advertised as 2x50bp but in reality is 2x61bp using a 8bp dual index (61|8|8|61) ...what is the '61' number equivalent for the SP500 kit when using a 8bp dual index?

TIA...I wasn't able to find this online.

*edited for clarification

Answer 1

[GenoMax]

That number is 538 cycles.

See this bulletin for information for all kits: https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000007002

[noodle]

Thank you so much! ...and part 2 of that question - is there a limit on how reads can be split between R1 and R2?

For example, can I have 500|8|8|22 ? Are you aware of technical limits of the machine or practical limits in terms of base quality?

*edit I also found this which indicates the max is 251bp, do you know if that is the hard limit? https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000002826

[GenoMax]

No there is no limit but you will be working outside performance spec. Make sure your library will support that kind of sequence configuration. If sequencer runs out of library to sequence the run may crash. Illumina will not comp kits on crash for non-standard usage like this.

[noodle]

I just added an edit, I've never run the SP500 kit but I read on another post that 251bp is the max, is that an actual hard limit that the machine won't let you go over? Or just the Illumina documented advise?

https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000002826

[GenoMax]

Far as I know there were instances in past where people had run 600 cycles in one direction for a 300 cycle kit. If Illumina is now limiting that in software then you will find that out if you try to set a run up like one you refer to above.