Nanopore sequencing, Shasta toolkit enable de novo assembly of 11 human genomes

Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by z991 on Tuesday May 05, 2020 @06:58PM (#23086112)

Oxford Nanopore (makes the sequencer used here) is one of my favorite companies. I think we'll see their work start to change how we do diagnostics in the next 5 years, especially with their automated library preparation product [1].

I was blown away how possible billion-base DNA sequencing is in non-lab environments when we bought one of these for fun [2].

[1] https://youtube.com/watch?v=x-z3MFkpvzE&t=1m20s

[2] https://abarry.org/dna-sequencing-in-our-extra-bedroom/

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Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by refurb on Tuesday May 05, 2020 @08:15PM (#23086601)

Highly entertaining write up! Hats off to you for attempting it (successfully!).

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Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by vikramkr on Tuesday May 05, 2020 @07:03PM (#23086143)

That's kind of epic that you managed to pull that off in a home setup. How exactly did you manage to run the gel and all? Did you buy a gelbox/agarose/dye etc too?

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Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by ejstronge on Tuesday May 05, 2020 @07:17PM (#23086233)

ONT have a ‘rapid’ kit that doesn’t require standard DNA lab equipment.

1. https://store.nanoporetech.com/us/sample-prep/rapid-sequenci...

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Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by vikramkr on Tuesday May 05, 2020 @07:24PM (#23086271)

The linked article in the patent comment talks about running a gel to confirm extraction which is what I was referring to

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Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by ejstronge on Tuesday May 05, 2020 @08:25PM (#23086672)

Thanks! I skimmed but noticed that they used the rapid kit - sorry!

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Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by z991 on Tuesday May 05, 2020 @07:36PM (#23086339)

We used the rapid kit and also a gelbox / agarose.

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Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by vikramkr on Tuesday May 05, 2020 @08:59PM (#23086883)

Did you end up buying everything? I'd be curious to know how much it cost overall if you'd be willing to share. While most of my time has been in well stocked academic labs or shared startup lab space, I did spend some time working out of a bio hacker space and I'm always curious how cost efficiently people can wrangle together enough otherwise expensive kit to run an experiment in an odd setup. Did you end up with a lot of extra agarose etc or were you able to resell the leftovers and the used kit? Super cool stuff.

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Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by z991 on Wednesday May 06, 2020 @12:46AM (#23087985)

In total it was about $3k. So not cheap, but also not a real lab budget by any means.

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