Jean P. Elbers

What about using it for ruSTAR output summaries ?

Oops, meant upstream or before, but I would need to write a script that corrects the lengths of sequences in the overlap PAF file to match the length of the sequences in the FASTA file.

Well, after using rawsamble, the first big problem using it downstream of RACON or HERRO is the overlaps are based on the signals, and the length of the reads may differ in the .paf files compared to the actual length of the basecalled sequences.

Wow, thanks. Will try it.

Thanks for a super cool tool! · Issue #1 · GZHoffie/skiver Hi, Thank you for developing such a cool tool. I used it on a 30x human nanopore ultra-long read set for the "same" read identifiers and modifying a script in the skiver-test repository, was able t...

Do you think it can do something like these seaborn heatmaps with labels though github.com/GZHoffie/ski...

Do you recommend Salmon or piscem for bulk-RNAseq these days? Salmon always made more sense to me to map reada to the transcriptome than align to the genome for bulk-RNAseq.

Rawsamble: Overlapping Raw Nanopore Signals using a Hash-based Seeding Mechanism AbstractMotivation. Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the s

This looks really interesting and perhaps might enable faster overlapping for HERRO @msikic.bsky.social , not sure academic.oup.com/bioinformati... , also not sure Rawsamble can overlap repetitive sequences, for which minimap2 can, but seems to slow down a lot compared to default settings

Introducing kuva: A scientific plotting library in rust, along with cli binary with the option to plot directly into the terminal.

Feel free to drop me some feedback as an issue on the repo

github.com/Psy-Fer/kuva

crates.io/crates/kuva/...

Vibe coding as a term was coined I think in February 2025, and I saw a job posting looking for someone with 2+ years in vibe coding experience. I know that people were vibe coding with large language models before the term existed but give me a break.

Hang in there...

I did not point out though that it sends the hashing sketch to a JGI(?) server.

Maybe try Brian Bushnell's sendsketch.sh . It has refseq and uses hashing bbmap.org/tools/sendsk...

But at the moment, @nanoporetech.com needs to make new clair3 models in pytorch for #SUP version 5.2.0 with move table support #nanopore

www.biorxiv.org/content/10.6... Clair3 v2 for #nanopore reads, it keeps getting better!

www.biorxiv.org/content/10.6... with html link

Looks interesting...https://www.biorxiv.org/content/10.64898/2026.02.12.705514v1 Skiver: Alignment-free Estimation of Sequencing Error Rates and Spectra using (k, v)-mer Sketches

Hare 0.26.0 released

Hare 0.26.0 Released

- Loop values and for..else
- #DragonflyBSD support
- Explicit syntax for ignoring errors when needed
- Replacing @offset with fields named _ for padding structs
- Support for explicitly uninitialized variables

harelang.org/blog/2026-02...

#HareLang

Forgot to tag #nanopore if anyone has that tag in his/her feeds

Does this help? There have been some additional optimizations from the ONT Machine Learning Team with dorado and Ada Lovelace and Blackwell GPU architectures. github.com/Kirk3gaard/2...

@badphysicist.bsky.social

GitHub - uutils/coreutils: Cross-platform Rust rewrite of the GNU coreutils Cross-platform Rust rewrite of the GNU coreutils. Contribute to uutils/coreutils development by creating an account on GitHub.

I hate how slow GNU Core Utilites `tar` can be with unzipping gzipped tar balls. I wonder if you could make a pull request to the rust core utilites github.com/uutils/coreu... that integrated mim (if possible) into its ruTar?

Oh, that seems great! And performance?

I would say rust-htslib as @johanneskoester.bsky.social and team are actively working on it. Not to say the developer of noodles is not working on noodles. Just my two cents.

Unlocking the full potential of nanopore sequencing: tips, tricks, and advanced data analysis techniques Abstract. Nucleic acid sequencing is the process of identifying the sequence of DNA or RNA, with DNA used for genomes and RNA for transcriptomes. Decipheri

From @narjournal.bsky.social #NARCriticalReviewsAndPerspectives | Unlocking the full potential of #nanopore sequencing: tips, tricks, and advanced data analysis techniques | #Bioinformatics #Genomics #OpenScience #NGS #OxfordNanopore 🧬 🖥️🧪🔓
⬇️
academic.oup.com/nar/article/...

Took me way too long to realize that its super easy to just merge pdfs in R rather than fussing with Adobe #rstats

library(pdftools)
pdf_combine(
input = c("file1.pdf", "file2.pdf"),
output = "merged.pdf"
)

Sounds like making automated quizzes would be very useful!

I wonder about claude code or some LLM making the quiz.md files for you?

Is it microbial data? If so, Squid Base has you covered. squidbase.org Other wise maybe @kirk3gaard.bsky.social can chime in on the ENA.

...Yeah, but all of the C libraries you can directly call/use so easily in #Ziglang.

I think you would have to use a cloud instance to get the Nvidia Blackwells like those.