On Saturday, January 10, 2015 at 8:53:45 AM UTC-8, phillyj wrote:
Sorry, I meant HiSeq lane of course, not MiSeq (the MiSeq flowcell is essentially a single lane). But even a Miseq should be able to multiplex four bacterial genomes or so on a single cell.
The HiSeq does two flowcells per run, with 8 lanes per cell. Mick Watson has a good analysis here:
Given that that was written in 2013 and I'd expect costs have gone down slightly since, you can probably translate £ to $ and not be all too far off. But even at £126 per genome, that'd be only $190 for a de novo sequenced bacterial genome, library prep included. That's an awesome deal, provided we can find a supplier that is offering that kind of service to us DIYbio folks!
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Can you explain what you mean by a single MiSeq lane? Our lab has Life
Tech Ion Protons so I'm a little familiar with that. It's not my area
so I only know a little bit about the NGS setup.
The HiSeq does two flowcells per run, with 8 lanes per cell. Mick Watson has a good analysis here:
The rapid-run mode of the HiSeq 2500 is perfectly capable of producing 150 million 150bp paired-end reads. This equates to 45Gb of sequence data.
If we are sequencing 5Mb genomes, at 40X, we need 200Mb of sequence. 96 of those will therefore need ~20Gb of sequence, so as you see, a single lane of HiSeq 2500 easily copes.
ARK-Genomics runs a non-profit full cost recovery business model, which means we charge for reagents, staff time and equipment. So for that lane of sequencing, we would probably charge in the region of £2500.
We need to factor in the cost of libraries. In reality, we could make this cheaper via automation, but for the sake of ease, let's say the library prep is £100 per sample. That's £9600 on library prep.
That's a total of £12100, or £126 per genome.
In reality, I think we could get library prep down to £50 per sample, This would bring the cost down to £76 per genome.
Patrik
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