how much will it cost to sequence a bacterial genome on the promethion?

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.


3 thoughts on “how much will it cost to sequence a bacterial genome on the promethion?

  1. @biomickwatson makes the excellent point that staff costs and compute costs for promethion are probably higher. I decided not to address these as it opens up various cans of worms.

  2. Those homopolymer errors are going to be brutal, especially with a genome strongly skewed for G+C. But perhaps for assessing absence/presence of genomic islands & such it could be useful alone

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