ASeq Newsletter

The ASeq Newsletter explores advancements and challenges within the sequencing technology landscape, focusing on industry dynamics, clinical applications, and market competition. It critically examines the role of major companies like Illumina, emerging technologies, and the impact of sequencing in diagnostics and oncology.

Sequencing Technology Genetics and Diagnostics Market Dynamics Clinical Applications Industry Analysis Technological Innovations Company Profiles

Top posts of the year

And their main takeaways

A Qitan Technology Nanopore Data Release

7 implied HN points • 17 Nov 23
  1. Qitan Technology released E.Coli K12 and human cell line datasets under 'Demo Data' on their website.
  2. The read length distribution appears promising, with reasonably long reads.
  3. Q scores from the released data suggest limited calibration to Q25, but show a lower overall error rate compared to previous publications from Qitan.

Maybe Nanopore Protein Sequencing Is Easier Than I Thought?... Maybe Not?...

7 implied HN points • 12 Mar 24
🔬 Science Sequencing
  1. Protein sequencing can potentially be easier than expected with nanopore technology, allowing for detection of PTMs and obtaining unique fingerprints from proteins.
  2. Proteomics differs from DNA sequencing in that it allows for estimating protein abundance and identifying PTMs in samples, possibly through aligning multiple protein traces.
  3. Challenges in proteomics applications with nanopore platforms include achieving the necessary dynamic range for accurate measurements, which may require advancements in technology.

Reticula Patent Search Reports!

7 implied HN points • 18 Nov 23
  1. Reticula Patent Search Reports share innovative ideas for single cell sequencing and error rate reduction
  2. Long read single molecule sequencing can improve quality consensus without phasing issues
  3. Original Reticula approach for nucleic acid sequencing uses a novel dye removal method without fluidics

Oxford Nanopore Error Rate Is >5%?

7 implied HN points • 07 Nov 23
  1. The Oxford Nanopore error rate may be higher than 5%
  2. To find the overall error rate of Oxford Nanopore data, alignment of the data is necessary
  3. Quality scores seem well calibrated up to Q20, but errors rise significantly beyond that

Compute In The MiSeq and Ion Torrent PGM

7 implied HN points • 23 Oct 23
  1. Ion Torrent PGM and MiSeq are similar instruments released around 2010.
  2. They use different technical approaches resulting in different architectures.
  3. The embedded compute in these instruments varies significantly.
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Thoughts On Ultima Genomics...

0 implied HN points • 07 Feb 24
  1. Ultima Genomics focuses on affordability for high throughput users.
  2. Illumina may respond with lower pricing to compete with Ultima Genomics.
  3. PPMSeq by Ultima Genomics offers a promising approach worth monitoring.

Everything Wrong With: "Illumina: The Measurement Monopoly" Part 5/8

0 implied HN points • 03 Jan 24
  1. During the early 2000s, Illumina faced competition from companies like Pacific Biosciences, 454 Life Sciences, and Solexa Inc.
  2. Other sequencing startups existing back in 2005 included Reveo, SeiRad, DNA Electronics, Intelligent Biosystems, Complete Genomics, and Oxford Nanolabs.
  3. 454 Life Sciences and Solexa were the primary platforms showing data at the time, with Helicos and PacBio launching later.

Macklemore: Next-gen Sequencing Evangelist

0 implied HN points • 03 Nov 23
  1. Macklemore is a leading figure in next-gen sequencing, revolutionizing the field
  2. Macklemore believes that PacBio's Revio is the new clinical standard in human genetics
  3. PacBio and the Revio could become the new clinical standard in whole genome sequencing

Oxford Nanopore Acquires Northern Nanopore Instruments

0 implied HN points • 07 Nov 23
  1. Oxford Nanopore acquired Northern Nanopore Instruments, known for solid state nanopore research tools.
  2. Northern Nanopore used controlled breakdown approach for creating small nanopores in silicon membranes.
  3. Vincent Tabard-Cossa lab's method involved applying voltage slowly until membrane breakdown occurred, then modulating voltage post-breakdown.

That New Nanopore Protein Sequencing Paper

0 implied HN points • 24 Oct 23
  1. The study designed synthetic proteins for nanopore sequencing with the ClpX unfoldase.
  2. Results showed single amino acid changes in a static context with some classification efficiency.
  3. Challenges remain in sequencing proteins due to the complexity of possible states and electron limitations.

Oxford Nanopore Simplex Error Rate STILL >5%?

0 implied HN points • 08 Nov 23
  1. The Simplex Error Rate for Oxford Nanopore is still greater than 5%.
  2. Despite some slight improvement in accuracy, the overall error rate is at 5.74%.
  3. Current accuracy of Oxford Nanopore seems to be worse than first generation Illumina sequencers.