I may have responded to you with this before, if so, sorry, lots of duplication the last couple of days.
A friend of mine searched this out for 5 minutes, nanopore is not all that cool.
"I have literally looked into Nanopore for all of 5 minutes so take this with a grain of salt. There may be there better evidence out there, but just from…
I may have responded to you with this before, if so, sorry, lots of duplication the last couple of days.
A friend of mine searched this out for 5 minutes, nanopore is not all that cool.
"I have literally looked into Nanopore for all of 5 minutes so take this with a grain of salt. There may be there better evidence out there, but just from this first paper I found from December 2020, Nanopore doesn't look as great as Couey made it out to be:
Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis
"However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to COMMON CONCERNS AROUND SEQUENCING ACCURACY."
"Although protocols for ONT sequencing of SARS-CoV-2 have been established and applied in both research and public health settings20,21,22, adoption of the technology has been LIMITED DUE TO CONCERNS AROUND ACCURACY. ONT devices exhibit LOWER READ-LEVEL SEQUENCING ACCURACY than short-read platforms23,24,25. This may have a disproportionate impact on SARS-CoV-2 analysis, due to the virus’ low mutation rate (8 × 10−4 substitutions per site per year26), WHICH ENSURES ERRONEOUS (false-positive) OR UNDETECTED (false-negative) GENETIC VARIANTS HAVE A STRONG CONFOUNDING EFFECT."
It looks like they use synthetic RNA references as well as mapping to the original genome to "confirm" accuracy so it seems that they must have a reference first:
"Synthetic DNA or RNA REFERENCE STANDARDS can be used to assess the accuracy and reproducibility of next-generation sequencing assays27. We first sequenced synthetic RNA controls that were generated by in vitro transcription of the SARS-CoV-2 genome sequence. The controls matched the Wuhan-Hu-1 reference strain at all positions, allowing analytical errors to be unambiguously identified. To mimic a real-world viral WGS experiment, synthetic RNA was reverse-transcribed then amplified using multiplexed PCR of 98 × ~400 bp amplicons that enabled evaluation of ~95% of the SARS-CoV-2 genome. Eight independent replicates were sequenced on ONT PromethION and Illumina MiSeq instruments (see Methods section).
We ALIGNED THE RESULTING READS TO THE WUHAN-HU-1 REFERENCE GENOME TO ASSESS SEQUENCING ACCURACY and related quality metrics (Supplementary Fig. 1a–i). Illumina and ONT platforms exhibited distinct read-level error profiles, with the latter characterised by an elevated rate of both substitution (23-fold) and insertion-deletion (indel) errors (76-fold; Table 1 and Supplementary Fig. 1d,"
"With ONT sequencing known to exhibit higher read-level sequencing error rates than short-read technologies23,24,25, REASONABLE CONCERNS EXIST ABOUT SUITABILITY OF THE TECHNOLOGY FOR SARS-CoV-2 GENOMICS. Moreover, public databases for SARS-CoV-2 data (e.g., GISAID: https://www.gisaid.org/) already contain consensus genome sequences generated via ONT sequencing, POTENTIALLY CONFOUNDING INVESTIGATIONS THAT RELY ON THESE RESOURCES."
The researchers claim that their article resolves the concerns around Nanopore so it would be interesting to investigate if any other teams confirmed this. In any case, if they must rely on synthetic RNA reference standards as well as the fraudulent original genome created from metagenomics in order to create and confirm the accuracy of the Nanopore sequence, it seems Couey's evidence is off to a very bad start.
as I said there are is no evidence that chains of base pairs from Nanopore, whole genome or Sanger sequencing relates to any entity or means anything at all.
I may have responded to you with this before, if so, sorry, lots of duplication the last couple of days.
A friend of mine searched this out for 5 minutes, nanopore is not all that cool.
"I have literally looked into Nanopore for all of 5 minutes so take this with a grain of salt. There may be there better evidence out there, but just from this first paper I found from December 2020, Nanopore doesn't look as great as Couey made it out to be:
Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis
"However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to COMMON CONCERNS AROUND SEQUENCING ACCURACY."
"Although protocols for ONT sequencing of SARS-CoV-2 have been established and applied in both research and public health settings20,21,22, adoption of the technology has been LIMITED DUE TO CONCERNS AROUND ACCURACY. ONT devices exhibit LOWER READ-LEVEL SEQUENCING ACCURACY than short-read platforms23,24,25. This may have a disproportionate impact on SARS-CoV-2 analysis, due to the virus’ low mutation rate (8 × 10−4 substitutions per site per year26), WHICH ENSURES ERRONEOUS (false-positive) OR UNDETECTED (false-negative) GENETIC VARIANTS HAVE A STRONG CONFOUNDING EFFECT."
It looks like they use synthetic RNA references as well as mapping to the original genome to "confirm" accuracy so it seems that they must have a reference first:
"Synthetic DNA or RNA REFERENCE STANDARDS can be used to assess the accuracy and reproducibility of next-generation sequencing assays27. We first sequenced synthetic RNA controls that were generated by in vitro transcription of the SARS-CoV-2 genome sequence. The controls matched the Wuhan-Hu-1 reference strain at all positions, allowing analytical errors to be unambiguously identified. To mimic a real-world viral WGS experiment, synthetic RNA was reverse-transcribed then amplified using multiplexed PCR of 98 × ~400 bp amplicons that enabled evaluation of ~95% of the SARS-CoV-2 genome. Eight independent replicates were sequenced on ONT PromethION and Illumina MiSeq instruments (see Methods section).
We ALIGNED THE RESULTING READS TO THE WUHAN-HU-1 REFERENCE GENOME TO ASSESS SEQUENCING ACCURACY and related quality metrics (Supplementary Fig. 1a–i). Illumina and ONT platforms exhibited distinct read-level error profiles, with the latter characterised by an elevated rate of both substitution (23-fold) and insertion-deletion (indel) errors (76-fold; Table 1 and Supplementary Fig. 1d,"
"With ONT sequencing known to exhibit higher read-level sequencing error rates than short-read technologies23,24,25, REASONABLE CONCERNS EXIST ABOUT SUITABILITY OF THE TECHNOLOGY FOR SARS-CoV-2 GENOMICS. Moreover, public databases for SARS-CoV-2 data (e.g., GISAID: https://www.gisaid.org/) already contain consensus genome sequences generated via ONT sequencing, POTENTIALLY CONFOUNDING INVESTIGATIONS THAT RELY ON THESE RESOURCES."
https://www.nature.com/articles/s41467-020-20075-6
The researchers claim that their article resolves the concerns around Nanopore so it would be interesting to investigate if any other teams confirmed this. In any case, if they must rely on synthetic RNA reference standards as well as the fraudulent original genome created from metagenomics in order to create and confirm the accuracy of the Nanopore sequence, it seems Couey's evidence is off to a very bad start.
the video in the link I posted is very cool.
as I said there are is no evidence that chains of base pairs from Nanopore, whole genome or Sanger sequencing relates to any entity or means anything at all.