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Old 05-22-2019, 08:19 PM   #3
Location: USA

Join Date: May 2019
Posts: 10

Originally Posted by luc View Post
I guess it is not the throughput nor the lifespan of the instruments that kills the older sequencers; it is mostly the comparatively high costs per base. The exception are the MiSeqs because Illumina has not bothered to develop a new longer read sequencer.
Is it correct to think of the cost per base savings as tied to the reductions in consumable costs due to the new 2 channel sequencing method?

It seems that at the beginning of 2017, the customers most suited to switching from HiSeq to Novaseq were core labs, industry/pharma labs and diagnostics that need a lot of throughput. They could benefit from the consumable cost reductions. The smaller customers, not so much.

James Hadfield talks about that in his 2017 post here. But that's two years old now. Has much changed? Are the small and medium labs phasing out their HiSeqs?

According to Illumina there is a $2-4 per Gb difference ($16/18 vs $20) for NovaSeq S1/S2 flowcells versus HiSeq 4000. This is a reduction of 10-20% on current costs for consumables only. The price per million reads please is less clear as the costs of S1/S2 flowcell kits has not been released.

NovaSeq may be economical when service contracts are taken into consideration. A fleet of 2500ís could be replaced with 1 NovaSeq saving significant sums on those expensive HiSeq contracts. But this will reduce a pretty good revenue stream for Illumina as the numbers of NovaSeq in the field is unlikely to hit the highs of the 2500!

Overall costs are likely to drop for users as NovaSeq replaces HiSeq 2500 and 4000, and cannibalises HiSeq X Ten. But those costs apply primarily to consumables. As sequencing prices continue to plummet, library-prep costs get higher and higher (relatively speaking). Today library is at least 50% of the cost of doing RNA-Seq of ChIP-seq. In the future it might be as high as 75% of the cost. We desperately need library-prep innovation!
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