Lucas van Dijk @lucasvandijk.nl · 23/07/2026What a huge achievement! 450 human haplotypes. PacBio Kinnex transcriptomic data, Fiber-Seq (nucleosome occupancy), and so much more! 042
Lucas van Dijk @lucasvandijk.nl · 11/06/2026It’s really ridiculous how quickly it flags anything biology or bioinformatics 030
Reposted by Lucas van DijkPacBio @pacbio.bsky.social · 26/05/2026SPRQ-Nx chemistry is now shipping worldwide, bringing sub-$300 HiFi genomes to the Revio platform! This global rollout cuts sequencing costs by 30%, making it easier than ever to scale high-throughput workflows Full press release here: bit.ly/49HwmcL #SPRQNx #PacBio #HiFisequencing #Revio 0147
Reposted by Lucas van DijkAlex Crits-Christoph @acritschristoph.bsky.social · 27/04/2026oh that's very very cool: 13410
Lucas van Dijk @lucasvandijk.nl · 22/04/2026I'm still working on semi-global alignment, though it's currently a "personal time" project so I can't give a timeline for that yet. Claude has been helpful though recently :) 010
Lucas van Dijk @lucasvandijk.nl · 22/04/2026Is global alignment sufficient? I am working on a new POASTA version with a Ukkonen-style band doubling strategy here: github.com/broadinstitu... Global alignment seems to work pretty well, but not extensively tested yet.github.comGitHub - broadinstitute/poasta at banded-poaFast and exact gap-affine partial order alignment. Contribute to broadinstitute/poasta development by creating an account on GitHub. 200
Lucas van Dijk @lucasvandijk.nl · 11/04/2026Independent of “coding being largely solved” (which I think is definitely hype), coding is only one part of a software engineer’s job. I’d argue that system architecture and design is not yet solved, and in my experience current LLMs are still not great at coming up with the right data abstractions. 290
Reposted by Lucas van DijkRichard McElreath 🐈⬛ @rmcelreath.bsky.social · 11/03/2026So what's the most interesting, or weirdest, application of hidden markov models (HMMs) that you've seen? I once built an HMM for sage grouse mating behavior, fit to data collected by a robotic grouse (pictured doi.org/10.1086/703518). Looking for other examples for a new lecture on HMMs. 1714421
Lucas van Dijk @lucasvandijk.nl · 30/11/2025That x86 ABI mug is going to be powering my mornings :) 140
Lucas van Dijk @lucasvandijk.nl · 28/11/2025I am very excited to have started a new role as a senior software engineer at @pacbio.bsky.social! I’ll be joining the instrument analysis team developing high-performance software on instrument delivering those beautiful HiFi reads to you 😁 250
Reposted by Lucas van DijkMike Schatz @mikeschatz.bsky.social · 14/10/2025Getting excited for #ASHG25. The must see talk is tomorrow at 1:30 by Qiuhui (Iris) Li presenting the first large-scale integration of long-read genome sequencing with electronic health record data across >1000 All of Us participants meetings.ashg.org/event/ASHG25...meetings.ashg.orgPheedLoopPheedLoop: Hybrid, In-Person & Virtual Event Software 1439
Lucas van Dijk @lucasvandijk.nl · 07/10/2025>1,000 human genomes sequenced with PacBio HiFi, offering many new insights into human structural variation and its associations with disease. www.medrxiv.org/content/10.1...medrxiv.orgPopulation-scale Long-read Sequencing in the All of Us Research ProgramThe All of Us Research Program (AoU) is a national biobank seeking to enroll one million individuals in the United States to link genomic and biomedical data, including short- and long-read whole-geno... 010
Lucas van Dijk @lucasvandijk.nl · 27/07/2025Easier might be to use “basedpyright” which has built-in uv environment detection support. 030
Reposted by Lucas van DijkErik Garrison @thinks.lol · 17/07/2025Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested! 12830
Reposted by Lucas van DijkAlexandria Ocasio-Cortez @aoc.bsky.social · 03/07/2025I am grieving the barbarism that is going to unfurl from all this. People are going to die. Livelihoods gone. All to feed a corrupt kleptocracy. I see every day up close how different it is from the first time around. There are no guardrails. A disaster. I’m sorry we have to live through this. 34849983121746
Lucas van Dijk @lucasvandijk.nl · 17/02/2025Spain spent 57 bln euros to build its entire high speed rail network. www.theguardian.com/commentisfre...theguardian.comSpain’s high-speed trains aren’t just efficient, they have transformed people’s lives | María RamírezA fiasco like HS2 could never happen here – our fast train network is so popular that no Spanish government would dare give up on it, says journalist María Ramírez 010
Lucas van Dijk @lucasvandijk.nl · 11/02/2025And now officially out in Oxford Bioinformatics :) academic.oup.com/bioinformati...academic.oup.comFast and exact gap-affine partial order alignment with POASTAAbstractMotivation. Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pa 1131
Lucas van Dijk @lucasvandijk.nl · 09/02/2025Thanks to @jdidion.bsky.social for writing 99% of the tree-sitter grammar at the heart of this extension. I made some modifications to ensure compatibility with Zed's WASM plugin system and fixed a few bugs in the C lexer extension. 000
Lucas van Dijk @lucasvandijk.nl · 09/02/2025For those using WDL for their bioinformatic workflows: I wrote an extension for the @zed.dev code editor enabling syntax highlighting and integration with wdl-lsp. It also supports bash highlighting in command blocks. Installable through the Zed extensions pane! github.com/broadinstitu... 150
Lucas van Dijk @lucasvandijk.nl · 27/01/2025A printed thesis! Did not expect it would feel so good to have the final version physically in your hands 🙌 120
Reposted by Lucas van DijkNature Reviews Genetics @natrevgenet.nature.com · 27/01/2025Diversity and consequences of structural variation in the human genome go.nature.com/4awEtaY #Review by Ryan L. Collins & Michael E. Talkowski @broadinstitute.org @harvard.edu @harvardmed.bsky.socialgo.nature.comDiversity and consequences of structural variation in the human genome - Nature Reviews GeneticsCollins and Talkowski provide a broad overview of structural variation in the human genome that covers their mutational properties, the dynamics of population genetics and functional consequences in d... 2267
Reposted by Lucas van Dijkqntm @qntm.org · 17/01/2025COMPUTER SCIENTISTS: "k" means one thousand and twenty-four STORAGE MANUFACTURERS: "k" means one thousand DISPLAY MANUFACTURERS [thinking hard]: "K" means nine hundred and sixty 621811299
Lucas van Dijk @lucasvandijk.nl · 10/01/2025That looks super interesting and I would read that in a heartbeat! 010
Reposted by Lucas van DijkTravis Wheeler @wheelerlab.org · 07/01/2025Still in beta, so possible minor API changes ... but our Suffix Array library (in Rust) is ready for business. Builds on lovely ideas in CaPS-SA from @robp.bsky.social. Low mem construction. Spaced seeds. Optional crazy-low-mem search. More info on the horizon. 0115
Reposted by Lucas van DijkMing Tommy Tang @tommytang.bsky.social · 07/01/20255/ In my experience, most of the time, you don’t need deep learning. Often, simple methods like linear regression or random forests work well — especially for moderate-sized datasets. Deep learning excels in image analysis & protein structure prediction. 3192
Lucas van Dijk @lucasvandijk.nl · 12/12/2024I remember this blog: kobzol.github.io/rust/cargo/2... But it was released earlier this year, so not super recent.kobzol.github.ioMaking Rust binaries smaller by defaultHave you ever tried to compile a helloworld Rust program in --release mode? If yes, have you seen its binary size? Suffice to say, it’s not exactly small. Or at least it wasn’t small until recently. T... 110
Lucas van Dijk @lucasvandijk.nl · 25/11/2024Anyone insight how I can configure pylsp such that it finds and autocompletes packages installed with uv? 000
Lucas van Dijk @lucasvandijk.nl · 19/11/2024ChatGPT when you ask it to write something clearly and succinctly: "Salutations and felicitations, sir, and a most jocund welcome to the sink. I am your electronic valet and household central processor. May I be of service, sir?" 010
Lucas van Dijk @lucasvandijk.nl · 19/11/2024Found ChatGPT in Fallout New Vegas: "Are you some kind of AI?" "Regrettably not, sir. All modules in this habitat are synthetic personalities atop a mundane operating system. There is no intelligence here, sir." www.youtube.com/watch?v=4XJw... 110
Reposted by Lucas van DijkBluesky @bsky.app · 15/11/2024💡 Tip: You can set your website as your username on Bluesky! This is one form of self-verification, and we especially encourage official organizations and brands to do this! Examples include @npr.org @react.dev @duolingobrasil.com.br. Here's our guide for how to do this:bsky.socialHow to set your domain as your handle - BlueskyUsing a domain as your handle helps with account identity, verification, and portability. Here's how to set your domain as your handle. 1445366396770
Lucas van Dijk @lucasvandijk.nl · 16/11/2024“Liberal democracy,” he says, “offers moral constraints without problem-solving” — a lot of rules, not a lot of change — while “populism offers problem-solving without moral constraints.” 000
Lucas van Dijk @lucasvandijk.nl · 16/11/2024This piece that includes a conversation with a professor of autocracy who’s an Hungarian exile has some strong points in my opinion (gift article) www.nytimes.com/2024/11/15/o...nytimes.comOpinion | This Is the Dark, Unspoken Promise of Trump’s ReturnLiberal democracy offers moral constraints without problem-solving. Populism offers problem-solving without moral constraints. 210
Lucas van Dijk @lucasvandijk.nl · 15/11/2024Every time I watch a HBO doc on a cult (The Vow, Love Has Won, Breath of Fire, Synanon, …), I’m taking notes 📝 020
Lucas van Dijk @lucasvandijk.nl · 14/11/2024It took me nearly a week to figure out why the BAM generated by a coworker gave different results than one that I generated myself 😱 To prevent this, we manually specified the fragment length mean with BWA's -I flag in future analyses. 100
Lucas van Dijk @lucasvandijk.nl · 14/11/2024If a downstream task filters improperly paired alignments (which is pretty common), it might filter accurate alignments that just happened to be in a batch with few other reads that aligned. 100
Lucas van Dijk @lucasvandijk.nl · 14/11/2024By increasing the batch size, successfully estimating the fragment length mean and std will be more likely! Thus, it is more likely to have fewer improperly paired reads. 100
Lucas van Dijk @lucasvandijk.nl · 14/11/2024Now, what happens when you increase the number of threads in BWA? It will multiply the read batch size by the number of threads, distributing read alignment over each thread and processing more reads in parallel! 100
Lucas van Dijk @lucasvandijk.nl · 14/11/2024In that case, -all- aligning reads in that batch will be marked as improperly paired, even if the alignments are accurate. 100
Lucas van Dijk @lucasvandijk.nl · 14/11/2024Here's the kicker: if the species of interest in a metagenomic sample is at low abundance, occasionally so few reads will successfully align to the reference that BWA cannot estimate the fragment size mean and std. 100