Nanoporing a human genome
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Andreas "Mega" Stuermer
Apr 3, 2018, 5:22:14 PM4/3/18
to DIYbio
Hi!
We are going to sequence a human genome with a nanopore in the Ars Electronica. We want to compare this to the genome sequence that a commercial company provides us with.
Any input which company offers full genome sequencing for a low price? Highly appreciated
Skyler Gordon
Apr 4, 2018, 12:37:17 AM4/4/18
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Hello,
I like your idea!
Oxford Nanopore (O.N.) long read technology is great for deciphering portions of the genome that would usually go unnoticed - such at short tandem repeats and homopolymers - and is also great for creating long contiguous sequences (or “contigs”) that can then be used to align to one another more accurately.
That being said, the accuracy of base calling just isn’t the same with the Nanopore read technology.
Today, most labs doing full genome sequencing are using O.N. to generate a skeleton genome map and then using Illumina sequencing to “polish” the map with more accurate sequence data.
There is a company in the United States (Texas) called “Mr. DNA”. They sequence pretty much what ever you send them.
There are also numerous genomics sequencing “cores” at universities and institutes around the United States that supplement their research with funding from sequencing. UCSD and The Scripps Research Institute both have DNA sequencing cores that provide Illumina and Oxford Nanopore technologies.
-SG
I like your idea!
Oxford Nanopore (O.N.) long read technology is great for deciphering portions of the genome that would usually go unnoticed - such at short tandem repeats and homopolymers - and is also great for creating long contiguous sequences (or “contigs”) that can then be used to align to one another more accurately.
That being said, the accuracy of base calling just isn’t the same with the Nanopore read technology.
Today, most labs doing full genome sequencing are using O.N. to generate a skeleton genome map and then using Illumina sequencing to “polish” the map with more accurate sequence data.
There is a company in the United States (Texas) called “Mr. DNA”. They sequence pretty much what ever you send them.
There are also numerous genomics sequencing “cores” at universities and institutes around the United States that supplement their research with funding from sequencing. UCSD and The Scripps Research Institute both have DNA sequencing cores that provide Illumina and Oxford Nanopore technologies.
-SG
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David Murphy
Apr 4, 2018, 2:42:22 AM4/4/18
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How many nanopore units do you have? They keep going until they die- the pores get blocked or the custom proteins around the pore degrade but the read quality is so crap you need significant depth to get anything usable.
Last time Oxford nanopore came round to give a presentation they were very keen to tell us about some projects where it was used on bacterial genomes but a quick back of the envelope estimate based on genome size implied that you'd need something like $50 - $100K worth of disposable nanopore units to get anything worth a damn.
They're also not the only game in town when it comes to long read tech. PACbio is a bit overhyped but the cost vs quality ratio seems much more realistic right now.
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David Murphy
Apr 4, 2018, 2:47:46 AM4/4/18
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Sorry. Forgot to add the sequencing link.
I don't know if they do individual samples or what the prices are like on small jobs but try looking for a quote here:
Andreas "Mega" Stuermer
Apr 6, 2018, 2:48:49 PM4/6/18
to DIYbio
Thank you guys, we also found Dante labs, they claim yo offer WGS for ~800$
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