
Nanopore sequencing, Shasta toolkit enable de novo assembly of 11 human genomes - bookofjoe
https://www.nature.com/articles/s41587-020-0503-6
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z991
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](https://youtube.com/watch?v=x-z3MFkpvzE&t=1m20s)

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

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

1\. [https://store.nanoporetech.com/us/sample-prep/rapid-
sequenci...](https://store.nanoporetech.com/us/sample-prep/rapid-sequencing-
kit.html)

~~~
vikramkr
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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z991
We used the rapid kit and also a gelbox / agarose.

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vikramkr
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.

~~~
z991
In total it was about $3k. So not cheap, but also not a real lab budget by any
means.

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enricotal
Shasta produced a complete haploid human genome assembly in under 6 hours.

I found out the record is 100 minutes.
[https://www.biorxiv.org/content/10.1101/705616v1.full](https://www.biorxiv.org/content/10.1101/705616v1.full)

The improvement could be that it is done on a single commercial compute node.

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zmmmmm
It's a bit frustrating (and concerning?) that their data repository [1] seems
incomplete; the most important seqences (GM12878 / HG001) are missing from
everything but the raw data directory. This is the sample that most
laboratories would likely have readily available for comparison to their
results, but for some reason they have omitted to deposit their final results
for it (unless I'm missing something ...).

[1] [https://s3-us-west-2.amazonaws.com/human-
pangenomics/index.h...](https://s3-us-west-2.amazonaws.com/human-
pangenomics/index.html?prefix=)

~~~
vikramkr
Is it in any of the supplementary information or in any of the figure source
data links in the paper? They do link in addition to the AWS open data this
link
([https://www.ebi.ac.uk/ena/data/search?query=PRJEB37264](https://www.ebi.ac.uk/ena/data/search?query=PRJEB37264))
- did you look through that? Other than that now idea - seems like a bit of an
oversight from nature if they wouldn't make sure important sequences were
readily available, you'd imagine they'd be important for peer review as well
prior to publication.

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anticensor
a.k.a. days of gene-edited humans.

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vikramkr
This is a faster sequencing technology, not a faster gene editing technology.

And the days of gene edited humans have been here for a while now. Gene
therapy trials have been running for decades, fda approved in 2017 ish, etc

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anticensor
Faster sequencing will enable faster gene editing turnarounds by faster
mutation detection.

