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Old 11-20-2014, 08:11 AM   #1
Kyubi
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Default Mate-pair sequencing service

Hi all,

Iv got 23 contigs (unpaired reads) (estimate 2.5mb long does any one know of a cheap mate-pair sequencing service that i can use to scaffold my genome (how much does it usually cost??) and any cheap alternatives
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Old 11-20-2014, 10:13 AM   #2
Brian Bushnell
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You should also consider running 2 PacBio SMRT-cells and redoing the assembly rather than generating LMP and scaffolding. We generally get microbes in 1 contig with 2 cells, which is not too expensive (~$200 each, plus some other costs). And with a 2.5Mbp genome, 2 cells is plenty.
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Old 11-20-2014, 11:00 AM   #3
Kyubi
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Thanks for the information, i am intereseted in using Pacbio but do you know of any place that could provide the service for around ~400, as most of the sequencing services seem to cost considerably more
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Old 11-20-2014, 11:03 AM   #4
Brian Bushnell
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Oh, I'm just talking about internal costs, I have no idea how much places charge for it, after labor and markups, etc.
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Old 11-20-2014, 11:10 AM   #5
GenoMax
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@Brian: Did you mean to say $2000?

On http://genohub.com, cheapest price I see for a 2 cell run (sequencing only, no library prep) is $800. All rest of the providers are $2000 and up for 2 cells.
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Old 11-20-2014, 11:17 AM   #6
Brian Bushnell
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No, I mean internally, the cost is estimated at around $200 per smart cell, excluding library prep and maybe some reagents, and depreciation/opportunity cost of the machines, etc. So certainly the real cost is a lot higher, and at a for-profit center would be higher still to customers, but 2 smart cells are considered cheaper for us compared to an LMP library, which is vastly more labor-intensive in addition to the costs of consumables. Then again, they way accounting is done does not always realistically reflect true costs.

So, $800 for sequencing 2 cells sounds reasonable for a for-profit center to offer with a minimal profit margin. The machines (and their time, maintenance contracts, etc) are expensive.

Last edited by Brian Bushnell; 11-20-2014 at 11:20 AM.
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Old 11-22-2014, 05:13 AM   #7
Kyubi
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Hi thanks for the help, i spoke to some companies that provide different types of sequencing services i managed to get the cheapest price for pacbio to $1900. I also managed to get a quote for optical mapping for half the price (but of course id need to do some sanger sequencing to complete the genome if i use the optical map service).

Considering i have 23 contigs and the nucleotide coverage is about 99.7% do you think optical mapping would be cost effective in the end??, has any one used this service for scaffolding and checking quality of assembly and do they have any pros and cons as compared sequencing methods??

Last edited by Kyubi; 11-22-2014 at 05:30 AM.
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Old 11-22-2014, 02:48 PM   #8
GenoMax
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With PacBio you would have a good chance of finishing the genome (with productive libraries, of course). I have no experience with optical mapping and can't say if that option would offer similar odds.
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Old 11-22-2014, 05:56 PM   #9
Brian Bushnell
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Quote:
Originally Posted by GenoMax View Post
With PacBio you would have a good chance of finishing the genome (with productive libraries, of course). I have no experience with optical mapping and can't say if that option would offer similar odds.
I agree. Similarly, I have no experience with optical mapping, but I do know that when we sequence a bacteria with 2 SMRT-cells, we usually end up with a single contig, unless of course the organism has additional plasmids.

Since you already have such a nearly-complete genome it's unfortunate to have to completely resequence it. But, I will say one thing...

2.5 Mbp is extremely small. With a single SMRT-cell, using the latest chemistry, if you have good yield (at least 80x coverage, or ~200Mbp) you will probably get a 1-contig assembly. Down to 60x... maybe 1 contig, more likely 2.
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Old 01-13-2015, 08:30 PM   #10
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Default PacBio Sequencing Services

Posting the services and costs mentioned in this thread, 2 PacBio SMRT Cells: https://genohub.com/shop-by-next-gen...6112c23d7121d3. These are sequencing costs only, click on library prep and sequencing filter for both. Click on view details to initiate a project.
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