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The next frontier in NGS is long read SMRT (Single Molecule Real Time - PacBio) combined with Oxford Nanopore's technology. That is, very long reads combined wi

by aroch 11y ago

The next frontier in NGS is long read SMRT (Single Molecule Real Time - PacBio) combined with Oxford Nanopore's technology. That is, very long reads combined with massively parallel transcription that doesn't rely on light emission. Illumina-based tech is not going to be part of the equation. Illumina is really only related to traditional Sanger sequencing in that its sequencing by synthesis.

adenadel 11y ago
There is no way that this is going to be the case. It's much more likely to be a combination of Illumina and ONT or ONT alone. PacBio is far too expensive and low throughput to be a challenger outside of niche applications (like genome assembly).
- aroch 11y ago
  I would much rather have ONT backed by Pacbio than ONT backed by Illumina. ONT is well suited for doing WES quickly, with better fidelity than Illumina and PacBio is much better for supplemental data to do genome assembly using reads from a short read system
  - adenadel 11y ago
    What evidence do you have for ONT having better fidelity than Illumina in any application? Illumina's error rates are typically <= 1% while on "good" reads ONT has error rates cited at 15% and overall is even worse[1]. I agree that PacBio is better for genome assembly, but for many cases we do not need to do assembly. Resequencing workflows with alignment and variant calling are pretty good. 1. http://www.sciencedirect.com/science/article/pii/S2214753515000224 http://www.sciencedirect.com/science/article/pii/S2214753515...
- epistasis 11y ago
  I'm extremely skeptical that ONT's sequencing will become cost effective. Library preps for long range correlation + Illumina will likely dominate; why not get high fidelity + long range off the same instrument and reagents? Dovetail and 10X are two companies doing this right now. That or a different nanopore tech. After all the time they've spent and the missed promises of ONT's CEO it doesn't look like the current generation will deliver.

by aroch 11y ago

adenadel 11y ago

There is no way that this is going to be the case. It's much more likely to be a combination of Illumina and ONT or ONT alone. PacBio is far too expensive and low throughput to be a challenger outside of niche applications (like genome assembly).

aroch 11y ago
I would much rather have ONT backed by Pacbio than ONT backed by Illumina. ONT is well suited for doing WES quickly, with better fidelity than Illumina and PacBio is much better for supplemental data to do genome assembly using reads from a short read system
- adenadel 11y ago
  What evidence do you have for ONT having better fidelity than Illumina in any application? Illumina's error rates are typically <= 1% while on "good" reads ONT has error rates cited at 15% and overall is even worse[1]. I agree that PacBio is better for genome assembly, but for many cases we do not need to do assembly. Resequencing workflows with alignment and variant calling are pretty good. 1. http://www.sciencedirect.com/science/article/pii/S2214753515000224 http://www.sciencedirect.com/science/article/pii/S2214753515...
epistasis 11y ago
I'm extremely skeptical that ONT's sequencing will become cost effective. Library preps for long range correlation + Illumina will likely dominate; why not get high fidelity + long range off the same instrument and reagents? Dovetail and 10X are two companies doing this right now. That or a different nanopore tech. After all the time they've spent and the missed promises of ONT's CEO it doesn't look like the current generation will deliver.