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Old 05-01-2016, 04:36 AM   #1
sebl
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Default Minimum run output and quality

Hello,

I hope this is the right place to ask this.

I was asked to write the terms for a tender for a NGS service provider for our institute.

We aim to work mainly with whole genome sequencing/re-sequencing of bacteria and viruses.

The question is how may I specify the minimum parameters of output and quality below which it would be reasonable to require (demand?) that the service provider perform a run again without charge?

I mean, what is the minimum % of the expected output for any type of run (say, Illumina) below which a run is considered invalid? Same for average quality? Other parameters that should be included (run parameters)?

Thank you!
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Old 05-01-2016, 04:43 PM   #2
GenoMax
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Take a look at http://allseq.com/ and https://genohub.com/ to get an idea of what is out there. The guarantee's are going to vary from provider to provider.

Yields from typical Illumina runs are published in the specs for each instrument (e.g. http://www.illumina.com/systems/hise...fications.html you can search for other sequencers). You need to keep in mind that these specs are for "normal" (uniform A/C/T/G distribution) samples and while they are achievable with regular samples the quality of the libraries has to be excellent to get this sort of output. You have not said if you will be making the libraries or expect the provider to make them. Quality libraries will generate quality output.

Ultimately the level of service may depend of the volume of samples you have available. Larger volumes will give your more flexibility. But if the volume is low then don't expect a lot of leeway.
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Old 05-02-2016, 01:06 AM   #3
sebl
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Hi,

Thanks for the links. From Genohub:

Quote:
Unless otherwise specified in the quote, the provider agrees to deliver pass filter reads that are at least 85%.
So, if I got it right, let's say we are talking about a Miseq run with V2 chemistry. Illumina specs. are
Quote:
>75% bases higher than Q30 at 2x250 bp
. So the sequencer in Genohub would guarantee for minimum 85% or of the 75% expected output?
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Old 05-02-2016, 01:17 AM   #4
sebl
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Oh, and I mean that lib prep would be included in the service.
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Old 05-02-2016, 03:39 AM   #5
GenoMax
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Quote:
Originally Posted by sebl View Post
Hi,

So, if I got it right, let's say we are talking about a Miseq run with V2 chemistry. Illumina specs. are . So the sequencer in Genohub would guarantee for minimum 85% or of the 75% expected output?
Yes. Achievable with normal/good libraries (no low nucleotide diversity).

Be sure to include sample QC in your request since that will likely be an added cost. It may sometimes be worth paying that upfront since you will know which samples are not worth processing for libraries.
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Old 05-02-2016, 04:36 AM   #6
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Good point, thanks!
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