Software breakthrough radically boosts the speed of nanopore DNA sequencers

If anyone is interested in DNA sequencing, I think the WENGAN paper [0] that came out the other day is pretty interesting too. They are using a hybrid input [1] in combination with their software package to reconstruct higher fidelity reference genomes.

The big impact from that paper is really summarized by this:

> WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 80.64 Mb (NGA50: 59.59 Mb), which surpasses the contiguity of the current human reference genome (GRCh38 contig NG50: 57.88 Mb)

[0] https://www.nature.com/articles/s41587-020-00747-w

[1] Long and short reads, for example from Nanopore and Illumina, respectively

Re: Software breakthrough radically boosts the speed of nanopore DNA sequencers

#8

Post by wiz21c » Thu, Dec 17, 2020, 7:27 PM UTC

alextheparrot wrote: post #7

If anyone is interested in DNA sequencing, I think the WENGAN paper [0] that came out the other day is pretty interesting too. They are using a hybrid input [1] in combination with their software package to reconstruct higher fidelity reference genomes. The big impact from that paper is really summarized by this: > WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 80.64 Mb (NGA50: 59.59 Mb), which…

until with have AlphaGenome (they'just beaten some protein folding problem by a laarge margin).

(I didn't look in the specifics of the problem so it may be completely wrong, but, you know, these days ...)

Re: Software breakthrough radically boosts the speed of nanopore DNA sequencers

#9

Post by PunchTornado » Thu, Dec 17, 2020, 7:44 PM UTC

xiphias2 wrote: post #5

jgmmo wrote: post #4

Note - this is NOT about whole genome sequencing.

Can it be used instead of PCR Covid test for example?

we already have covidseq by illumina which does this at a pretty big scale and provides survaillence and diagnostics in one test.

the issue is that PCR still is the cheapest and fastest way to get the results.

Re: Software breakthrough radically boosts the speed of nanopore DNA sequencers

#10

Post by myhf » Thu, Dec 17, 2020, 7:44 PM UTC

xiphias2 wrote: post #5

jgmmo wrote: post #4

Note - this is NOT about whole genome sequencing.

Can it be used instead of PCR Covid test for example?

This would be me more applicable to looking for variants of a known gene. For example, measuring mutation rates within known covid-positive samples.