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Old 09-02-2014, 03:04 AM   #1
Polinices5
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Default Outsourcing genome assembly

Hi All,

I am looking to outsource the sequencing, assembly and annotation of a relatively small (~150mb) eukaryotic genome.

I've seen lots of posts here about sequencing strategies and costs. But what is the reasonable end product to expect from a sequencing facility? Will it be a fasta file? Annotated, complete chromosomes (I realize this is unlikely)? A gff file?

Does anyone have experience outsourcing all of this, and if so can you tell me what you got in the end?

Of course, any recommendations of stellar sequencing facilities are welcome too!

Thanks.
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Old 09-02-2014, 09:42 AM   #2
Brian Bushnell
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I recommend the Joint Genome Institute because it's both stellar and free! But, we only accept proposals that are judged to have adequate scientific merit and good experimental design, so you have to apply. And for eukaryotes, we focus on plants and fungi.

As for output, you typically get a fasta assembly and annotated predicted genes (gff or similar), as well as the mapped reads. You will NOT get annotated complete chromosomes; that requires effort in the $1m to $10m range, I think, though I'm not sure exactly where in that range a 150MB organism would fall.

Last edited by Brian Bushnell; 09-02-2014 at 09:49 AM.
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Old 09-02-2014, 10:44 AM   #3
GenoMax
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As a side note, JGI releases all data publicly (http://jgi.doe.gov/collaborate-with-...view/policies/).

You can outsource the sequencing and assembly (though you could try to do this yourself). But the annotation may best be handled by the subject matter expert i.e. you. If a close relative has been sequenced then things could progress quickly, once you get the sequence/draft assembly.
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Old 09-03-2014, 01:52 AM   #4
mwatson
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Hello!

The answers to all of your questions really depend on many factors. We'd be happy to answer all of these, simply fill in our new project enquiries form:

http://genomics.ed.ac.uk/contact-us/new-project-enquiry

Thanks!

Mick
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Old 09-04-2014, 04:57 AM   #5
Polinices5
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Hi all,

Thanks for your replies. I realize there are lots of different ways to go about this, but I am asking because I want to know what sort of bioinformatics skills we might need if we contract this out.

Is it normal to receive a fasta file that needs to be annotated? Or if we contract for annotation, how complete is this likely to be?

We already have RNAseq data for the same species, so our main goal is to be able to map that onto the "genome". What will we need to do to the "genome" files before we can map onto them? Or what should we be asking for so that we can perform this most easily?

Thanks!
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Old 09-04-2014, 05:30 AM   #6
mwatson
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Hello!

With the greatest respect in the world, and I mean that, the assembly and annotation of genomes is a complex job that can take many months, if not years - even if it is only 150Mb in size. The Drosophila genome is 170Mb and is still being annotated today, 14 years after it was first published.

When you ask what needs to be done it a genome before you can map RNA reads to it, this makes me think that perhaps you need quite a bit of bioinformatics training. Given your level of expertise, I would not recommend that you attempt the assembly and annotation yourself.

I again welcome you to use our project enquiry form, and we will be able to help you out

Many thanks
Mick
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Old 09-04-2014, 05:36 AM   #7
Polinices5
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Thanks for the reply Mick,

Your answer illustrates exactly why I'm asking this community about what to expect. I have a tiny bit of bioinformatics experience, enough to know that this is a huge job to expect from a core facility (but they are offering it!).

So, when contracting out library preparation, sequencing, and initial bioinformatics can anyone tell me what they've received in return? I have no shortage of offers by labs to take my money, but no idea what I will get in the end!

Has anyone who has sent of DNA for a "draft genome" tell me what they got back?

Best
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Old 09-04-2014, 05:39 AM   #8
mwatson
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Hello!

What you get back depends on what you pay for - this is not an easy question to answer unless you provide more details.

For example, if you have $1million, then you can pay for a team of bioinformaticians spend years to produce a fantastic assembly and annotation. If you have $100, then you get the results of some automated software.

This is why I ask you to fill in the form. Answers to your questions are meaningless until we understand the project better

Mick
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