What do you think of this idea?

[Jeswin]

Hi Andreas,
I have an idea. Can we make this a DIYbio group effort and release the sequence data to the public? As I am reading on this, it looks like using Nanopore is not easy. Especially, the alignment and computational stage looks daunting to me. I also am busy with other projects and time is short. My proposal is below (I want to sent to DIYbio mailing list, but I need your approval before I email it). So please tell me if it is OK to email the DIYbio group?

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Idea: Community effort genome seq?

Andreas, our friend on the list, recently asked about using the Oxford Technologies Nanopore. I reached out because the lab I work for does have a Nanopore MiniIon. He proposed sequencing the Panellus stipticus genome to determine how to synthesize the fungal luciferase. I don't know if the sequence is publicly available or not. I like his proposal but I will have to convince the boss to carry this out. I don't really know how similar the Nanopore is to the Ion Proton NGS platform, in terms of cDNA library preparation or data analysis. It will be wonderful if the community came together to sequence an organism. I don't know how it can be done. If we can sequence the genome and make it public, I think it will be a big step for DIYbio. Time is of the essence for me.

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What do you think, Andreas?

Thanks,

Jeswin

--

In necessary things unity; in uncertain things freedom; in everything compassion.
-Marco Antonio Dominis

[Koeng]

What exactly would be required for this? What types of preps etc etc etc

[Jeswin John]

Oh great...i sent this to the mailing list instead of Andreas. O well.

The nanopore is supposed to be great for sequencing a whole genome because it reduces the time and cost. I am still doing research on it but based on some articles on the Oxford Nanopore Technologies (ONT) website, a whole genome can be sequenced more easily than current methods of shotgun sequencing or pyrosequencing. The species that Andreas had in mind was 50 megabases long. I am not sure how long that would take to sequence but I think you could get the whole genome in one run. Also, the price is uncertain. The nanopore flow cell is supposed to be $1000 with extra for reagents and labor. Whole genome sequencing is supposed to be sub-$1000 but I don't know if any company provides that for novel organisms.

Lastly, the ONT nanopore needs good computational tools to handle the data. I'm not sure how to create the whole genome for a novel organism.

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From: Koeng
Sent: ‎8/‎7/‎2015 11:06 PM
To: DIYbio
Subject: [DIYbio] Re: What do you think of this idea?

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