When Illumina announced the launch of MiSeq in January 2011 shortly before AGBT there was a lot of noise in the community on what this instrument might do. There was an equal amount of noise from companies offering competing systems and their early users. This peaked with a series of Ads from Ion Torrent
Just recently Keith Robison over at “Omics! Omics!” has been discussing whether Ion Torrent can keep its current first-mover advantage in the face of Illumina’s previous ‘form’ in this sort of competition. He mentions factors where the instruments might be compared and where differentiation might emerge: similar all-in purchase price, similar per-run cost, similar read lengths (with PE on Illumina only for now), similar numbers of reads. He also says that MiSeq looks like it will have “double the total output, faster runs and less hands on time or trouble”.
Lastly Keith discusses what Ion might do to keep ahead of the game. Well they have just released a hands-free ePCR system which will remove some of the pain. And the 318 chips with >400bp reads should yield well over 1Gb.
MiSeq was initially launched with specs of 1Gb of sequence in 24 hours and a cost of $125,000. The current spec is the same on Illumina’s website but also adds that about 3.4M reads will be generated per run. I went to AGBT, got the bag and attended the MiSeq launch party (free coffee, no booze). One of the things I picked up was a MiSeq flowcell. You can see one in the brochure and it is much smaller than a HiSeq flowcell, about 1/3rd the size.
It is not clear what area is being imaged right now but if MiSeq achieves the same cluster density and can utilise the new 600Gb chemistry then it may be possible to guess at where overall yield might go. I suggested back in June 2010 that HiSeq 2000 might generate 2Tb of data from a run. The audience thought this way over ambitious but we have already seen data from internal >1Tb runs from Illumina on that platform.
If we stick with 600Gb as the HiSeq run output or 75Gb per lane then a MiSeq lane (1/3rd the size of a HiSeq lane) might yield as much as 25Gb.
By my own estimates I’m still off by 100% on how much HiSeq might get to. And I’m suggesting MiSeq has room to grow 25x over its current 1Gb spec. Anyone interested in a sweepstake?