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Old 12-15-2017, 09:12 AM   #1
vebaev
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Location: Plovdiv, Bulgaria

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Default A Nanopore run - budget/cost?

As I'm not familiar with the whole protocol of a Nanopore run, can someone more experienced list the consumables/costs for a project concerning the run of unknown plant species genome DNA?

I'm aware of the following:
Nanopore - 1000$ (starter pack)
Covaris g-Tube - ~300$
...


Thanks in advance!
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Old 12-18-2017, 12:40 AM   #2
gringer
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Nanopore costs are all available on the nanopore store website. Here are some demonstrative figures:
  • Flow cells at their most expensive are $900 USD each
  • Kits are about $600 USD for six sequencing runs
  • Rough rule of thumb: $1000 USD per run (currently 1-15 Gb yield, depending on kit and input DNA quality)
  • Multiplexing is about another $300 USD for 12 runs of 12 samples (or 24 runs of 6 samples, etc.)
  • Wash kits are $200 USD for 12 flow cell washes (allow multiple runs per flow cell)

Most kits have example protocols on the website, so you can find out before you buy them what other reagents are needed.

If you have a particular experiment in mind, I can give you a better idea of what it will cost.
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Old 01-30-2018, 07:34 AM   #3
jhalpin
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I am also curious about costs. I'd like to run multiplex bacterial genomes and it looks like from the oxford site I can use either the 1d or 1d2 kit. Is it reasonable to run 12 4Mb genomes on one flow cell and expect good results? My math says yes, but I'd love to hear from someone with "real world" experience. We are interested in closing genomes and resolving large plasmids.

Each library kit is 6 reactions =~$100 per sample
Each barcode kit is 12 reactions =~$56 per sample

Is the pippin prep required for size selection? Are there other methods that can be used?
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Old 01-30-2018, 11:09 AM   #4
gringer
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The costs you have stated are per sequencing run, not per sample (i.e. $100 per run + $56 per run), so divide those numbers by six; please re-read the post that you replied to.

If bacterial genome sequencing is done from colonies, there should be no problems multiplexing 12 samples on each run. A 30X coverage Pseudomonas sequencing run multiplexed 12 times would need about 2 Gb of sequencing, which is achievable on the MinION with even the rapid kit.

This is the kit that can be used for that (including barcoding):

https://store.nanoporetech.com/catalog/product/view/id/226/s/rapid-barcoding-kit/category/28/

No Pippin prep needed; the transposase fragments the DNA and adds barcode sequence at the same time.

Ignore the costs stated on that product page, it's $672 for six runs of 12 barcodes (i.e. 72 samples in total), so $9.33 per sample for kit costs, and $75 per sample for flow cell costs (assuming the most expensive flow cell).

Last edited by gringer; 01-30-2018 at 11:18 AM.
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Old 01-30-2018, 12:07 PM   #5
jhalpin
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Thanks for the clarification.. I was having a hard time with Oxford's information on run vs sample.
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