naturepoker<p>ONT is finally fully discontinuing the original MinION Mk1B model (the original silver stick we're all familiar with). End of en era. I hope at least some future flow cells will continue to be compatible with the older platform 😔</p><p><a href="https://genomic.social/tags/microbiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>microbiology</span></a> <a href="https://genomic.social/tags/sequencing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>sequencing</span></a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
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#sequencing
2 posts2 participants0 posts today
#Molecular #epidemiology of #Kyasanur Forest Disease employing ONT-NGS a field forward #sequencing, https://etidiohnew.blogspot.com/2025/03/molecular-epidemiology-of-kyasanur.html
etidiohnew.blogspot.com#Molecular #epidemiology of #Kyasanur Forest Disease employing ONT-NGS a field forward #sequencing
What do #nanopore #sequencing #bioinformatics folks think about this one? New preprint on hashing raw nanopore signals and using them directly for de-novo assembly.
https://arxiv.org/abs/2503.02997v1
Hypothetical blow5-to-assembly pipe would be interesting, though figuring it out is way out of my depth.
arXiv.orgEnabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and TechniquesThe advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data present significant challenges related to accuracy, scalability, and computational efficiency. These challenges are mainly due to various forms of unwanted and unhandled variations in sequencing data, collectively referred to as noise. In this dissertation, we address these challenges by providing a deep understanding of different types of noise in genomic data and developing techniques to mitigate the impact of noise on genome analysis.
First, we introduce BLEND, a noise-tolerant hashing mechanism that quickly identifies both exactly matching and highly similar sequences with arbitrary differences using a single lookup of their hash values. Second, to enable scalable and accurate analysis of noisy raw nanopore signals, we propose RawHash, a novel mechanism that effectively reduces noise in raw nanopore signals and enables accurate, real-time analysis by proposing the first hash-based similarity search technique for raw nanopore signals. Third, we extend the capabilities of RawHash with RawHash2, an improved mechanism that 1) provides a better understanding of noise in raw nanopore signals to reduce it more effectively and 2) improves the robustness of mapping decisions. Fourth, we explore the broader implications and new applications of raw nanopore signal analysis by introducing Rawsamble, the first mechanism for all-vs-all overlapping of raw signals using hash-based search. Rawsamble enables the construction of de novo assemblies directly from raw signals without basecalling, which opens up new directions and uses for raw nanopore signal analysis.
2 prejudices I had on HMW extraction for long read sequencing:
I thought column kits were no good for HMW DNA, but latest Zymo miniprep(!) kits can do 15kb ~ >50kb
Apparently there are reliable pulse gel tools out there for resolving HMW bands, like FemtoPulse. Here's our miniprep at 14kb fragment size:
Every now and then, I look at trackers and then I come to my senses and then go nope.
More power to you if you like your vibrato values in hex but very, very nope.
I mean, they're a step forward from the MC4 and 8 but that's about it.
Pathogens often find their way into #wastewater & can be identified & quantified there by DNA #sequencing (widely known since COVID). Now research shows that this can be used as early warning system for outbreaks. https://www.theguardian.com/science/2025/mar/05/wastewater-disease-flu-outbreaks
The Guardian · Wastewater sampling could be key to early warning of new disease outbreaks
New entry of AI-generated #comics and #jokes added to our #website:
#Economic #Agreement #Sequencing
comics.lucentinian.com/4971
#DailyJokes #Jokes #LaughWithAI #DailyLaughs #VisitNow
comics.lucentinian.comEconomic Agreement SequencingWhy did the Ukrainian President rearrange the economic agreement? Because he wanted to throw the sequencing off!
Great blog post about new Roche's #Sequencing By Expansion (SBX).
Pre-print is also released already.
#nanopore
https://omicsomics.blogspot.com/2025/02/roche-xpounds-on-new-sequencing.html
https://doi.org/10.1101/2025.02.19.639056
omicsomics.blogspot.comRoche Xpounds on New Sequencing TechnologyBar bets can be a powerful force in human society. One of the best known books on the planet, The Guinness Book of World Records, originate...
DATE: February 24, 2025 at 09:00AM
SOURCE: BioWorld MedTech
Direct article link at end of text block below.
.@Roche looks to grow with #sequencing by expansion tech
#medtech @illumina
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t.coRoche looks to grow with sequencing by expansion tech
DATE: February 21, 2025 at 07:00PM
SOURCE: BioWorld MedTech
Direct article link at end of text block below.
.@Roche looks to grow with #sequencing by expansion tech
#medtech @illumina
Here are any URLs found in the article text:
Articles can be found by scrolling down the page at https://www.bioworld.com/topics/85-bioworld-medtech .
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Private, vetted email list for mental health professionals: https://www.clinicians-exchange.org
.
NYU Information for Practice puts out 400-500 good quality health-related research posts per week but its too much for many people, so that bot is limited to just subscribers. You can read it or subscribe at @PsychResearchBot
.
Since 1991 The National Psychologist has focused on keeping practicing psychologists current with news, information and items of interest. Check them out for more free articles, resources, and subscription information: https://www.nationalpsychologist.com
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EMAIL DAILY DIGEST OF RSS FEEDS -- SUBSCRIBE:
http://subscribe-article-digests.clinicians-exchange.org
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READ ONLINE: http://read-the-rss-mega-archive.clinicians-exchange.org
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t.coRoche looks to grow with sequencing by expansion tech
If I had my time again, this is one I would have given my left arm for.
Granted being left handed, that would possibly count against me.
Received invitation to submit a review article to an established academic journal - it'll be on a topic adjacent to long read sequencing analysis and #Archaea
Not too bad for a warehouse worker sequencing out of an artists' studio, IMHO! I'm feeling pretty nervous though.
Any good resources out there for first-time review article writers?
Discovery of #collagen in #fossil bone could unlock new insights into dinosaurs.
#protein #sequencing #paleontology #evolution #Edmontosaurus
https://phys.org/news/2025-01-discovery-collagen-fossil-bone-insights.html
Phys.org · Discovery of collagen in fossil bone could unlock new insights into dinosaurs
A novel #k-mer analysis tool based on next-generation #sequencing for foreign #DNA detection in #genome-edited products
https://phys.org/news/2025-01-mer-analysis-tool-based-generation.html
Phys.org · A novel k-mer analysis tool based on next-generation sequencing for foreign DNA detection in genome-edited products
For sequencing curious folks: a lab is trying to use up their last NextSeq 550 flowcell, and they're willing to run it for anyone for cost of the flowcell or less (likely a lot less).
Anyone interested in 30~39Gb worth of 150bp reads, let me know! We have about a week to figure this out.
Amateurs and independent researchers welcome too, but you'll have to extract your own DNA and send it to us.