Sequencing your DNA with a USB dongle and open source code
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Sequencing your DNA with a USB dongle and open source code
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Re: Sequencing your DNA with a USB dongle and open source code
#2This 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?
Re: Sequencing your DNA with a USB dongle and open source code
#3This 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?
Sounds like a fediverse project?
Re: Sequencing your DNA with a USB dongle and open source code
#4This 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 variants from the mapping results.
then compare your resultant vcf file to something like dbSNP: https://www.ncbi.nlm.nih.gov/snp/
at this point you can start generating a raw version of a 23andMe report.
Re: Sequencing your DNA with a USB dongle and open source code
#5This 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…
Nice! Thankyou for the links. I will research all of this.
Re: Sequencing your DNA with a USB dongle and open source code
#6This 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?
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.
Re: Sequencing your DNA with a USB dongle and open source code
#7Earlier quoted context omitted.
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…
Nice! Thankyou for the links. I will research all of this.
good luck! it’s not that tough, just a lot of new vocabulary.
Re: Sequencing your DNA with a USB dongle and open source code
#8This 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?
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.
Re: Sequencing your DNA with a USB dongle and open source code
#9Earlier 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.
The one I linked to is a decade out of date and OEM discontinued.
Re: Sequencing your DNA with a USB dongle and open source code
#10Earlier quoted context omitted.
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.
The one I linked to is a decade out of date and OEM discontinued.
ya my first thought was how hard are reagents to get, but probably not that hard. i wasn’t in the lab, i was in bioinformatics so i’m generally clueless on reagent acquisition.