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I expect us to use the long reads from ONT and PacBio to discover that structural variation is even more important and common than previously appreciated. If th

by eggie 9y ago

I expect us to use the long reads from ONT and PacBio to discover that structural variation is even more important and common than previously appreciated. If that's the case, you'd be silly to use the Illumina technology for anything more complex than population genetics, and this will probably trickle into many parts of the market as the medically-relevant parts of the field realize what the basic science is demonstrating.

jashephe 9y ago
The fact is, unfortunately, that Nanopore sequencing (and also, from what I’ve read, PacBio) has a dramatically higher error rate than Illumina sequencing-by-synthesis. In the near future, anyway, I would expect to see inaccurate PacBio/Nanopore long reads being used as scaffolds for accurate Illumina short reads (in fact, this is already happening). Illumina won’t be going anywhere any time soon.
- searine 9y ago
  >The fact is, unfortunately, that Nanopore sequencing (and also, from what I’ve read, PacBio) has a dramatically higher error rate than Illumina sequencing-by-synthesis. This is true, but only for Insertions/Deletions. The substitution error rate is comparable to Hi-Seq. So it's good for resequencing but without a reference or decent scaffolds, you're in the dark.
  - iskander 9y ago
    I've only sequenced a few samples on a MinION. The dominant error seemed to be miscounting the length of a homopolymer stretch (e.g. CCC->CCCCC) but the substitution error rate was also clearly worse than Illumina. I've gotten used to less than 0.1% error from DNA sequencing on a HiSeq 2500. My guess is that the MinION data had 1-3% substitution errors.
El_Montanero 9y ago
This is so cool. I'd been taught in high school that the human genome was no longer a mystery, and that science had fully decoded the entire thing. It seems pretty obvious now that the subtleties would be even more complex than we could have imagined.

by eggie 9y ago

jashephe 9y ago

The fact is, unfortunately, that Nanopore sequencing (and also, from what I’ve read, PacBio) has a dramatically higher error rate than Illumina sequencing-by-synthesis. In the near future, anyway, I would expect to see inaccurate PacBio/Nanopore long reads being used as scaffolds for accurate Illumina short reads (in fact, this is already happening). Illumina won’t be going anywhere any time soon.

searine 9y ago
>The fact is, unfortunately, that Nanopore sequencing (and also, from what I’ve read, PacBio) has a dramatically higher error rate than Illumina sequencing-by-synthesis. This is true, but only for Insertions/Deletions. The substitution error rate is comparable to Hi-Seq. So it's good for resequencing but without a reference or decent scaffolds, you're in the dark.
- iskander 9y ago
  I've only sequenced a few samples on a MinION. The dominant error seemed to be miscounting the length of a homopolymer stretch (e.g. CCC->CCCCC) but the substitution error rate was also clearly worse than Illumina. I've gotten used to less than 0.1% error from DNA sequencing on a HiSeq 2500. My guess is that the MinION data had 1-3% substitution errors.

El_Montanero 9y ago

This is so cool. I'd been taught in high school that the human genome was no longer a mystery, and that science had fully decoded the entire thing. It seems pretty obvious now that the subtleties would be even more complex than we could have imagined.