vep-rs: high-throughput Rust variant annotation with population-scale concordance to Ensembl VEP https://www.biorxiv.org/content/10.64898/2026.09.22.753614v1
Very excited to see my HFSP Long-Term Postdoc Fellowship featured in HFSP’s recent review! Thank you @hfspo.bsky.social for funding the coolest frontier science and for supporting my postdoc research @pauligroup.bsky.social and professional development. Check out their full report ⬇️
Human Frontier Science Program@hfspo.bsky.social · 2w agoWhat does #FrontierScience look like in practice? 🔬 7 case studies from the #HFSP Grand Review explore bold, high-risk research and the discoveries, collaborations and new directions that followed. 🧪 Explore the stories ➡️ zurl.co/wrwYg #sts #ResearchImpact
It's here! new preprint: Gravlax, an annotation-independent molecular evidence archive for scRNA-seq. A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵 www.biorxiv.org/content/10.6...
So who is going to be first to write a @nanoporetech.com basecaller using the Typesafe AI Jev API to read the squiggles from pod5 or blow5 files? Probably would not surpass Dorado, but well, you never know, right?
New #preprint : we introduce Phenotype Shift Scores (PSS), a pairwise framework for locating exceptional phenotypic differentiation across a phylogeny. Across 153 primate traits, morphology shows deeper-than-expected shifts.
A Framework for Quantifying DNA Methylation Heterogeneity and Detecting Co-methylated loci from Native Nanopore Sequencing https://www.biorxiv.org/content/10.64898/2026.09.07.749820v1
Meet the hellbender, North America’s biggest salamander, a walking water quality test, and the owner of a genome 16x bigger than that of human beings.
I am delighted to present with @hannespetur.bsky.social our new study on the Icelandic pangenome reference HPRC-ICE. This work goes all the way from pangenome construction to disease association! (1/7) www.nature.com/articles/s41...
An Icelandic pangenome reference - Nature
Newly developed methods enable construction of Icelandic haplotypes and mapping of population-scale short reads to a pangenome by reducing reference bias and improving discovery in low-mappability reg...
nature.com
@gbouras13.bsky.social talking about his new protein structure-based bacterial genome annotation tool, Baktfold. 🧫🧬 GitHub: github.com/gbouras13/ba... Preprint: www.biorxiv.org/content/10.6... #ISME20
We're having fun developing post-cloud bioinformatics tools: reimagining some of the bioinformatics canon as local, browser-native applications so your data never has to leave your laptop. Here's the first set: edwards.flinders.edu.au/viz/ Let us know if you want other tools local to your laptop
-viz
Welcome to the -viz suite of tools: classic bioinformatics tools, reimagined for the browser. agviz · bamviz · genbankviz · phispyviz Each of our tools is a classic bioinformatics tool, but reimagi…
edwards.flinders.edu.au
> DistSSHKit makes it easy to run one Julia project locally and over SSH, then collect the results… > These days, even small labs and individuals often have several high-performance machines or workstations. DistSSHKit helps you put that hardware to work. github.com/yamanori99/D... #JuliaLang
GitHub - yamanori99/DistSSHKit.jl: A Julia SSH execution kit that bundles remote setup, run, and result collection into one consistent workflow.
A Julia SSH execution kit that bundles remote setup, run, and result collection into one consistent workflow. - yamanori99/DistSSHKit.jl
github.com
1/ Excited to share our preprint ImpuT2T: a pangenome-based assembly patching tool ImpuT2T scaffolds draft human assemblies with a pangenome (HPRC2) and patches gaps by leveraging linkage disequilibrium and sequence identity between contigs and reference haplotypes Code: github.com/maojanlin/Im...
ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies
With improvements in sequencing and assembly have come many high-quality telomere-to-telomere assemblies and reference pangenomes. However, the long-read sequencing recipes needed for high quality ass...
biorxiv.org
ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies https://www.biorxiv.org/content/10.64898/2026.07.27.741037v1
Panomap: Unbiased Nanopore Signal Mapping with Pangenome Variation Graphs https://www.biorxiv.org/content/10.64898/2026.07.10.737796v1
Can anyone explain why Ubuntu with Linux Kernel 7.1.1 works with Nvidia Drivers 595.84 and a Nvidia RTX 3060, but Kernel 7.1.2 is not compatible with the that Nvidia driver? @phoronix-poster.bsky.social I can understand that Linux Kernel 7.2rc1 is not compatible but 7.1.2?
@nanoporetech.com , @vellamike.bsky.social , when will we see a SUP v6 model for Dorado v2?
For #bbm2026 folks - come check out my poster on 3FL, #21! It's part of the data going out on my soon-to-be published preprint, some aspects can definitely use feedback. 🧫🦠
With the #BYI announcement buzz settled, I’ve been reflecting on what this award means to me. 🎓 It’s a win for R2s, a boost for #wildlifegenomics 🐸🧬🖥️, and a testament to my @rittigers.bsky.social lab of students ✨ Reflections here: bit.ly/4xGNhX9 Thank you to @beckman-foundation.bsky.social!
Reflecting on the BYI: A Win for Salamanders, Mentorship, and the Road Less Traveled
If you had told me years ago that a career spent chasing salamanders through the woods would lead to being named a 2026 Beckman Young Investigator (BYI), I’m not sure I would have believed...
megalabrit.weebly.com
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
DynamicDemiLog: A Single Sketch for Ultrafast Similarity, Frequency, and Cardinality Estimation https://www.biorxiv.org/content/10.64898/2026.06.12.731986v1
The US Navy is using @nanoporetech.com sequencers in the field. www.wadsworth.org/news/wadswor... and defence--blog-com.cdn.ampproject.org/v/s/defence-... #nanopore
The Wadsworth Center Advises the U.S. Navy Core Genomics Laboratory on Forward-Deployed Pathogen-Agnostic Threat Detection | New York State Department of Health, Wadsworth Center
The Navy Force Health Protection Command (FHPC) is establishing a new Core Genomics Laboratory in Florida to enhance pathogen detection and genomic surveillance capabilities for forward-deployed milit...
wadsworth.org
Is @nanoporetech.com hac v6 better than 5.2.0 sup? The short answer is no. But are a few errors in a genome worth 5 times more basecalling compute? github.com/Kirk3gaard/M...
Nanopore sequencing provides not just long reads, but the the raw signal data can also be used to identify RNA and DNA modifications. This repository (and the associated review) lists some of the great tools that have been developed www.cell.com/trends/genet...
Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data
Nanopore sequencing provides signal data corresponding to the nucleotide motifs sequenced. Through machine learning-based methods, these signals are translated into long-read sequences that overcome t...
cell.com
Goeke Lab@goekelab.bsky.social · 4mo agoWe’ve updated our awesome-nanopore list! The list is a community-curated list of ONT software tools, please feel free to check it out & contribute: github.com/GoekeLab/awesome-nanopore #Nanopore #Bioinformatics #LongReadSequencing
Hey #genomics and #bioinformatics community: I need an "endorsement" in order to submit a preprint to @arxiv.bsky.social 😭 I'm registered, but can't submit our preprint to q-bio\GN (Genomics) section until we get an endorsement from an existing arXiv author w/endorse privileges. that you? plz DM me🙏
I've been working an a small Julia library for working with raw nanopore sequencing signals. It's still under development and not very mature, but maybe someone may find it useful and want to experiment with it. It provides functionality for signal-to-sequence alignments, basic signal scaling […]
Original post on mastodon.green
mastodon.green
NBD-VRAM Provides Swap Space On Your NVIDIA GeForce GPUs - https://www.phoronix.com/news/NVIDIA-NBD-VRAM
NBD-VRAM Provides Swap Space On Your NVIDIA GeForce GPUs
An open-source developer has created NBD-VRAM as a way to create swap space on your consumer NVIDIA GPU's video memory under Linux...
phoronix.com
github.com/sstadick/str... Stay in the code. Avoid context switching. That was the whole goal of this endeavor. I wanted to be able to use agents for things like search, one-off questions, and small patches without stepping out as abstracted as something like claude. github.com/sstadick/str...
