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#sequencing

1 post1 participant0 posts today
naturepoker

Minimod preprint from @hasindu2008 gang is out. Code available github.com/warp9seq/minimod

I love the work they're doing with slow5/blow5 open spec for ONT raw data, and archive all internal reads using them. Really need to sit down and test this one out with my #archaea raw data!

A bioinformatics tool for viewing and calculating base modification frequencies from BAM files - warp9seq/minimod
GitHubGitHub - warp9seq/minimod: A bioinformatics tool for viewing and calculating base modification frequencies from BAM filesA bioinformatics tool for viewing and calculating base modification frequencies from BAM files - warp9seq/minimod
#bioinformatics#methylation#ONT
Soh Kam Yung

"Researchers have described proteins that they say are among the most ancient ever sequenced. Two teams, which analysed molecules from extinct relatives of rhinos and other large mammals, have pushed back the genetic fossil record to more than 20 million years ago."

nature.com/articles/d41586-025

www.nature.comAncient proteins rewrite the rhino family tree — are dinosaurs next?Molecules from 20-million-year-old teeth are among the oldest ever sequenced.
#Proteins#Prehistory#Sequencing
naturepoker

1 of 2 posters for the summer picked up! I'll be presenting this one at upcoming Boston Bacterial Meeting #BBM2025.

A specific type of plasmid replication gene (RPA) is overreprented among Deinococcota & analysis hints at introduction of the MGE early in its history, tracing back to Allomeiothermus #microbiology #amateurbiology #sequencing

Since this is polishing up of such an older data, I'd say it's the most amateur-like (in a good way) of all stuff coming out of our warehouse lab right now

Daniel Hoffmann🌻

Whole genome #sequencing has become cheap enough to become a routine early diagnostic test for #rareDiseases. This can help patients to avoid years of fruitless diagnostic odyssey. Could also facilitate development of cures. Moving case report. nature.com/articles/d41586-025

www.nature.comWhole-genome sequencing susses out rare diseasesConventional tests that look only at a small subset of genetic code often miss variations hiding outside the protein-coding genome.
naturepoker

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.

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.
Jyoti Mishra

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.

#DAWs#Sequencing#CVGate
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