As a promethion looks comparable in startup cost with a MiSeq (though, actually, because the machine is free, you get more sequencing for your buck with the promethion), I wonder how much it would cost to sequence a bacterial genome on the promethion? This post involves a bunch of guesswork, extrapolation and the backs of envelopes, so ymmv. Corrections/improvements welcome.
Throughput per flowcell, promethion flowcells have 4x the pores of minion, so i’m assuming 4x the throughput. From a quick scan of the community site, 1 Gb of data from the latest pore/chem seems like a decent balance for optimism/realism. ONT have been spouting about 10Gbp, so I’m going to include an optimistic 5 Gbp per minion flowcell as well. Some people have reported this on the community.
Promethion flow cell throughput = 4 to 20 Gbp.
Cost per flowcell, on the PEAP docs, it says $91200 for 48 flowcells (I bet whoever decided to price in dollars rather than pounds is going to get a nice christmas bonus!), so
Promethion flow cell cost = $1900
Cost per Gbp of $95-$475.
Library prep costs, if assumed to be same as MinION = *** correction, it is $100 library prep per flowcell, so between $7-15 depending on plex *** dna is fragmented, barcoded, then used for library preparation
Add to that the cost of barcoding (each promethion flowcell is divided into 4 sample chambers, not 100% clear that these are distinguishable from the data, as the literature says that each flowcell is addressable, not each sample chamber). $24 per sample.
And a cost* per 50x bacterial genome (4 Mbp) of $26-$134. (edited to correct for library prep cost mistake)
Reminder that the $119 is very optimistic, and the $219 is definitely ‘on a good day’.
nanopore/lab experts – have i missed anything?
bioinformaticians – would you be happy with just nanopore data, with no illumina data to pilon? obviously you can use nanopore to call snps etc, see ebola & others, but to cut yourself off entirely from the comforting blanket of illumina re-assurance for whole bacterial genomes…
Remaining questions I have are:
- What will be minimum promethion flowcell order size/shelf life?
- What are the ‘official’ promethion flowcell throughput stats?
- How may people are in the promethion queue/how long would i have to wait if i ordered one now?
* i have used the term cost here, while Mick (who i like very much) points out that i should have been saying price.