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Sequencing your DNA with a USB dongle and open source code

stackoverflow.blog

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Re: Sequencing your DNA with a USB dongle and open source code

#101

Post by monopoledance »

inglor_cz wrote: post #44

DNA sequencing bugs me quite a bit. On one hand, I would love to learn something new about my body. On the other hand, what if the results tell me that I am predisposed to some horrible untreatable disease? Will I spend the rest of my days observing every little pain or discomfort and thinking "is this IT?"

I think you would have to two scenarios at hand:

1. A completely genetically determined disease; a rare 100%-going-to-happen deal. (Which you would probably know about already, because your mother, or grandfather died from it...)

2. Some significant, but abstract risk modification.

With 1., you would know, you will get sick/die some time soon in the future, allowing you to live your life accordingly, die without regrets, prepared and so on. You can take that into consideration when planning for a family, taking job offers, procrastinating on the good life with work and retirement plans. Burn bright.

With 2., there is a very, very high chance lifestyle choice influence the stated risk, as obviously not everybody who got the polymorphism gets sick. So you can get your ass up, exercise, quit smoking and drinking, reduce stress, get regular check ups, ..., and avoid getting sick or reduce the impact/progression, in case you do.

I think, logically, knowing is always better than not knowing. But I understand how anxiety does tell a different story.

Re: Sequencing your DNA with a USB dongle and open source code

#102

Post by pas »

mylons wrote: post #4
LinuxBender wrote: post #2

This is very cool. Are there by chance any associated projects that could evolve into something like 23andme but remain entirely within a private network meaning that the data is entirely in the hands of the individual?

yes. if you wanted to annotate your genome you could “easily” do it on your brand new macbook (this is ram intensive, you probably need 32G). you’d need a reference genome, like https://www.nist.gov/programs-projects/genome-bottle then you’d need a program like bwa http://bio-bwa.sourceforge.net/ to map your data. then use https://samtools.github.io/bcftools/howtos/variant-calling.h... or something else to produce va…

Could you please explain how this mapping works? Why it needs so much RAM? Is it doing a fuzzy search of sorts for known sequences (genes)? Why can't it do so one by one?

Re: Sequencing your DNA with a USB dongle and open source code

#103

Post by amelius »

Method-X wrote: post #79
m12k wrote: post #18

I'm really curious about what I could learn by getting my DNA sequenced, but I'm worried about my rights to not have it recorded and shared without my consent if I got someone else to do it for me - so any advance toward an affordable home test setup is very welcome.

When I had 23andme sequence my DNA, I used a fake last name and pre-paid credit card.

Uh yeah, but you logged in from an IP address which Google already tied to your real name.

Re: Sequencing your DNA with a USB dongle and open source code

#104

Post by pas »

joshuamcginnis wrote: post #40
ampdepolymerase wrote: post #6

Earlier quoted context omitted.

A used laboratory grade NGS system can be had for less than 10K https://www.ebay.com/itm/265148387179 Nanopore is still not quite ready yet for precise and high accuracy sequencing. Give it another five years.

That's not true. I just did a high-quality sequence and assembly of a new species of fungus from my home lab using nanopore. You can see all my code used for assembly and analysis that will be referenced in a paper I plan to publish in Jan here: https://github.com/EverymanBio/pestalotiopsis

How do you know the quality of the resulting sequence?

Re: Sequencing your DNA with a USB dongle and open source code

#105

Post by wombatmobile »

> Why not make the software into a proprietary product? ... There’s such a race there that it’s hard to commercialize the software for the long term.” Schatz continues, “Plus our work is largely funded through government sponsored grants, so this is one of the important ways for us to give back to society.”

In some people's thoughts, making a better society is the first and most obvious thing to do with technology like this, not an accidental consequence of inconvenience. Fortunately, enough of those people are active in the world to make Main Street different to Wall Street, at least sometimes.

Re: Sequencing your DNA with a USB dongle and open source code

#106

Post by haihaibye »

mylons wrote: post #8
ampdepolymerase wrote: post #6

Earlier quoted context omitted.

A used laboratory grade NGS system can be had for less than 10K https://www.ebay.com/itm/265148387179 Nanopore is still not quite ready yet for precise and high accuracy sequencing. Give it another five years.

wow i didn’t know they were that “cheap” now. i used to work for a major competitor to the sequencer you linked, the SOLiD. and i feel like nanopore is the VR of dna sequencing. it’s always just another few years off.

Occulus sold 8.1m units this year, more than XBox.

Re: Sequencing your DNA with a USB dongle and open source code

#108

Post by monopoledance »

GistNoesis wrote: post #72
dekhn wrote: post #45

Earlier quoted context omitted.

it's unlikely we would ever be able to achieve this. Even simulating a single cell at high resolution is a serious challenge.

It's likely that you don't have to simulate even a single cell at high resolution to be able to simulate how an organism would grow. There are numerical shortcuts. For example today we can already predict the color of the eyes and other phenotype from the DNA. If you are able to observe enough samples of cell growth and their associated DNA, you probably can model and predict the statistics of a cell from their DNA.…

> For example today we can already predict the color of the eyes and other phenotype from the DNA.

We could even do that, without knowing anything about DNA at all. Or predict tomorrows weather without satellites and computers.

I think you are a bit too enthusiastic about statistics, or too naive about complexity.

Re: Sequencing your DNA with a USB dongle and open source code

#109

Post by monopoledance »

323 wrote: post #59
dekhn wrote: post #45

Earlier quoted context omitted.

it's unlikely we would ever be able to achieve this. Even simulating a single cell at high resolution is a serious challenge.

You seriously underestimate the continuous growth of computer power. And quantum computers after, which are perfect for simulating chemical reactions. What was unthinkable 50 years ago, playing chess better than a human, it's now trivial for a $100 device. And it's not necessarily required that to simulate the growth of a human you'll need to simulate the entirety of chemical reactions in all 50 trillion cells and al…

You seriously underestimate the complexity of genetics and ontogenesis.

Re: Sequencing your DNA with a USB dongle and open source code

#110

Post by twotwotwo »

A researcher mentions using a compact index based on the Burrows-Wheeler Transform to fit things in less memory compared to using a huge hashtable.

I see open-source implementations of BWT-based indexes (FM-Index/FMtree) out there. Out of curiosity, does anyone know of anything using BWTs for compact indexes in more everyday uses (like full-text search), or alternately reasons it doesn't really work outside the genome-alignment use case? Likely it only 'pays for itself' if you really need the space savings (like, it's what makes an index fit in RAM) or else we'd see it in use more places. It'd still be kinda neat to actually see those tradeoffs.

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