Albert Vilella Profile picture
May 18 9 tweets 3 min read Twitter logo Read on Twitter
The tech update from Oxford @nanopore #NanoporeConf now ongoing with @The__Taybor now presenting:
Duplex: 1.5% of the time, the complement strand follows the first strand naturally.
Initially, modified the adapters and reached 30% duplex rate. Image
Stereo base caller uses similar ML approaches as ChatGPT, Image
Releasing "super-duplex" version today: 85-90% duplex rates, there may be room for improvement to 95%.
Duplex at Q32 with 5kHz measurements per second, rolling out now. Image
Duplex quality agnostic to read length, no light based chemistry that damages the DNA. Modal simplex at Q22 now, Modal duplex >Q30, longest Q30 read in the screenshot is 335kb (that's >20x longer than 15kb). Image
Native natural human DNA in current PromethION, above 50Gb, but also about another 50Gb of unpaired simplex. All the epigenetic modifications, damaged (signal to cancer?) is preserved. Image
There is now a version of the dorado basecaller supporting this Duplex base calling: intending to incorporate into MinKNOW in July 2023, but dorado binaries available to download from github. Image
Lots of advantages of duplex, e.g. assembly, higher accurate variation calling, etc. High-duplex available right now, look for R10.4HD in the website. Image

• • •

Missing some Tweet in this thread? You can try to force a refresh
 

Keep Current with Albert Vilella

Albert Vilella Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @AlbertVilella

May 17
On library prep at #Nanoporeconf, a description for PCR-free methods showing the difference between ligation (max output) and rapid mode (10minutes, minimal lab equipment needed). Ultralong reads (ULR) also enabled, all Kit14. Image
Rapid ULR. Current record is about 4 megabases. Image
PCR expansion kits enable the use of samples with low input amount. Image
Read 10 tweets
Apr 21
I did a deep dive on the different workflow management (WFM) tools for #Bioinformatics Data Analysis a few years ago, and since then there have been a few extra entrants in this segment, still mostly concentrated in serving the Next-Generation Sequencing field.
A few years ago, there were two communities dominating the open-source WFM ecosystem in NextFlow and SnakeMake, and two platforms dominating the the commercial offerings in DNAnexus and Illumina BaseSpace.
Since then, a company out of the founders of Nextflow has started offering enterprise support for Nextflow workflows in the cloud: Seqera Labs. They offer the extra level of support that some organizations require to run Nextflow on their Data Analysis setups.
Read 7 tweets
Apr 21
More interesting Next-Generation Sequencing knowledge in the ASeq Discord channel (by @new299). Illumina patterned flowcells and the etching process to "print" the wells into the flowcell. Could be down to 350nm diameter for some flowcell configurations now. Image
If I remember correctly, Illumina started with a 600nm diameter for the patterned flowcell, in the HiSeq X and then later on in the evolution of the platform that used these patterned flowcells.
They then said to have gone down to 500nm, and what you are showing seems to indicate that it's at 350nm now, at least for the NextSeq 2000? I am not sure if they claimed that for NovaSeq X?
Read 8 tweets
Apr 20
There have been some acquisitions in #CancerDiagnostics and #CancerScreening recently, some of which signify a trend towards consolidation that is worth describing:
$A Agilent is moving towards some more vertical integration in Cancer Dx and Cancer screening
by recently acquiring both announcing a partnership with Akoya Bio and announcing the acquisition of Avida Biomed. Image
Some may ask: isn’t $A Agilent too small to go into this field? Would they be able to compete against $ILMN Illumina/GrailBio or $GH Guardant Health or $EXAS Exact Sciences?
Read 4 tweets
Apr 20
It is likely that as Spatial Biology tools become more robust and user-friendly, they will become increasingly popular and widely adopted in the scientific community.
This may lead to a shift in the balance between single-cell and Spatial Biology approaches, with the latter eventually becoming more prevalent.
Additionally, as more and more datasets are generated using Spatial Biology techniques, the field of Machine Learning and Artificial Intelligence will likely play an increasingly important role in analysing and interpreting this data.
Read 6 tweets
Apr 19
A new post on Single Cell, Spatial Biology Omics and In situ Imaging on the URL in the image. Behind the curtain, some speculative thoughts on possible Mergers and Acquisition moves, including $TXG $NSTG and related companies such as $ILMN $GH $EXAS $RHHBY $ADAP $TMO $BDX , etc. Image
In recent years, methods for encapsulating individual cells and analysing their DNA, RNA or protein contents have become more established, with commercial support from Biotech and Life Science Tool providers
similar to what Next-Generation Sequencing received over the past decade or so. There is now a growing effort to transform academic lab-developed tools for Spatial Biology,
Read 55 tweets

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us on Twitter!

:(