NovaSeq 6000

The largest of the Illumina sequencing instruments, able to two flow cells independently of each other and generate massive sequencing depth at competitive prices.

Library pools can be sequenced on whole flow cells but also on individual lanes in which case there will be an extra cost for the XP workflow cluster kit in addition to the regular cost of flow cell and sequencing reagents.

The selection of different flow cells can be seen in the table below. Choice of flow cell will depend on a number of things:

• The amount of data needed per sample
• Number of available barcodes for the chosen library preparation method
• Nature of the libraries, such as fragment length, requirement for custom primers etc
• Required read-length

NGI coordinators will help you choose the best option for your project if you are unsure.

	Flow cell	Lanes	Yield (clusters/lane)	Read length
	SP	2	Minimal: ≥325M Typical: 500M	100 cycles (e.g. 2x50bp) 200 cycles (e.g. 2x100bp) 300 cycles (e.g. 2x150bp) 500 cycles (e.g. 2x250bp)
	S1	2	Minimal: ≥650M Typical: 900M	100 cycles (e.g. 2x50bp) 200 cycles (e.g. 2x100bp) 300 cycles (e.g. 2x150bp)
	S2	2	Minimal: ≥1650M Typical: 2000M	100 cycles (e.g. 2x50bp) 200 cycles (e.g. 2x100bp) 300 cycles (e.g. 2x150bp)
	S4	4	Minimal: ≥2000M Typical: 3000M	200 cycles (e.g. 2x100bp) 300 cycles (e.g. 2x150bp)

Quality scores:

• Greater than 85% of bases above Q30 at 2 × 50 bp
• Greater than 80% of bases above Q30 at 2 × 100 bp
• Greater than 75% of bases above Q30 at 2 × 150 bp

Minimal yield in the table above is what we guarantee if the libraries sequenced have passed our quality controls. Typical yield is based on what we get from most of the common library types made by us, but this can vary from case to case.

There will be a certain variation in yield between samples in a library pool depending on variations in pipetting and concentration measurements. NGI will accept a variation of +/- 25% between samples in a pool.

For most standard preps made at NGI we will try to fit your pool of libraries onto the S4 flowcell since it has the lowest price per sequenced base. Depending on the number of samples used and the number of available barcodes we will sequence projects down to quarters of lanes on the S4 flowcell. If for some reason this will not work the pool need to be sequenced on one of the smaller flowcells.

Below are some important exceptions:

• Pools with libraries not made by NGI always need to be sequenced on whole lanes
• Libraries in need of custom sequence and/or index primers need to be sequenced on flow cells
• Libraries in need of non-standard read setups (e.g. Chromium single cell) need to be sequenced on whole flow cells

Last Updated: 28th April 2020