Tue Sparholt Jørgensen
- Reposted by Tue Sparholt JørgensenTime for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
- Reposted by Tue Sparholt Jørgensen🦠🧬🖥️ Bakta v1.12.0 is out with tons of tiny improvements and bug fixes, too many to list all: - partial genes on linear seqs - improved errror handlings & runtimes - support Python 3.12 & 3.13 - ... A huge shout out and thank you to all bug reporters and contributors! github.com/oschwengers/...
- Reposted by Tue Sparholt JørgensenFirst fully phased reference genome for the Yarrowia liploytica type-strain is out! academic.oup.com/jimb/advance... Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well. #genomics
- Reposted by Tue Sparholt JørgensenNew tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates" 📄 www.biorxiv.org/content/10.6... 📦 github.com/marbl/anianns
- Reposted by Tue Sparholt JørgensenExploring #microbiome data? MetaTree makes statistically based hierarchical tree comparisons easy and accessible.
- My understanding of MDPI as the biggest polluter of science gets some quantitative basis in this cool study. How about we as researchers stop publishing there and stop reading it leaving the special issues with another issue: absence of honest science.
- For anyone interested, thread here 🙂 bsky.app/profile/hans...
- Reposted by Tue Sparholt JørgensenONT Axes P2 Solo, Roiling Community 🧬🖥️ omicsomics.blogspot.com/2026/01/ont-...
- Reposted by Tue Sparholt JørgensenNew blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued: rrwick.github.io/2026/01/21/p...
- Reposted by Tue Sparholt JørgensenUltra-high-throughput mapping of genetic design space www.nature.com/articles/s41... (read free: rdcu.be/eY6E2) 🧬🖥️🧪 github.com/cbashorlab/C...
- Unpacking my stuff in my new @ssi-dk.bsky.social office, I came across this post which resonated enough that I printed it out and hung it up on my wall. It's going back up now. I think from @danpsimpson.bsky.social ?
- Reposted by Tue Sparholt JørgensenBeen doing a lot of @nanoporetech.com sequencing for soil and sediment lately and it appears that no matter how much DNA or how little we still get decent yields. So pretty robust performance. Yield clearly depends on pore count.
- Reposted by Tue Sparholt JørgensenBacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive. Here we explore the conjugative capacity of these mysterious Genomic Islands. www.biorxiv.org/content/10.6...
- Reposted by Tue Sparholt Jørgensen
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated! - How delightful to start the year with a neat overview of the sequencing field from the most capable watcher of the space.
- Sequencing Instrumrnt Outlook 2026 My observations & predictions on sequencing instrument companies 🧬🖥️ omicsomics.blogspot.com/2026/01/sequ...
- Reposted by Tue Sparholt JørgensenSequencing Instrumrnt Outlook 2026 My observations & predictions on sequencing instrument companies 🧬🖥️ omicsomics.blogspot.com/2026/01/sequ...
- Reposted by Tue Sparholt JørgensenStaying Current in Data Science and Computational Biology: 2026 Edition. Part 3 in a series of posts going back 14 years. doi.org/10.59350/2na...
- Reposted by Tue Sparholt JørgensenNew preprint. Work led by @ainsley-beaton.bsky.social & Rebecca Devine. They show the highly conserved Streptomyces MtrAB two component system activates ectoine production and triggers sporulation in response to osmotic stress in Streptomyces venezuelae www.biorxiv.org/content/10.6...
- Reposted by Tue Sparholt JørgensenBorn #OnThisDay in 1922, Esther Lederberg was the first to isolate the lambda phage in 1951. She characterised the lysogenic phase, whereby the phage are able to integrate into the bacterial genome, staying dormant. This discovery made them a model tool of study, leading to many more breakthroughs.
- Reposted by Tue Sparholt Jørgensen💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...
- Reposted by Tue Sparholt JørgensenDNA is the best kind of time machine - really feels like we’re in a golden age of big data studies like this. Can’t wait to read!
- New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga). 🔗 DOI: www.biorxiv.org/content/10.6...
- Reposted by Tue Sparholt Jørgensen🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and @titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ? doi.org/10.1093/narg...
- Reposted by Tue Sparholt Jørgensen579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm
- Reposted by Tue Sparholt JørgensenHuge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
- Reposted by Tue Sparholt Jørgensen✨ New paper in Science: An archaeal genetic code with all TAG codons as pyrrolysine. www.science.org/doi/10.1126/... A collaboration with @innovativegenomics.bsky.social Congrats to the Banfield lab, @roeleah.bsky.social , @nxhamlish.bsky.social , and Alanna! #NSFfunded
- Once again inspiring work from Jillian Banfields group "An archaeal genetic code with all TAG codons as pyrrolysine" pasteur.hal.science/pasteur-0537...
- Reposted by Tue Sparholt JørgensenHot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...
- Reposted by Tue Sparholt JørgensenHappy to share our most recent work www.pnas.org/doi/10.1073/.... Here we describe how efficient DNA replication in E. coli is dependent on an interaction between SSB-ssDNA and the DNA polymerase (Pol III). Thanks to all the co-authors for their hard work!
- Reposted by Tue Sparholt Jørgensen“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6
- Reposted by Tue Sparholt JørgensenDid you know most 'complete' Streptomyces genomes are missing their telomeres? Thanks to David and Tues hard work, we now have a new tool to recover them! A pleasure to be part of a team. :) 🦠🧪💻 #microsky
- Bacterial telomeres are common, just not so much in RefSeq 'complete' genomes. But they can be added by the new tool David Faurdal wrote. I am thrilled to see this out as a preprint here: www.biorxiv.org/content/10.1... @tilmweber.bsky.social @thombooth.bsky.social
- Reposted by Tue Sparholt JørgensenI am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
- Reposted by Tue Sparholt JørgensenAround 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...
- Reposted by Tue Sparholt Jørgensen🚀 New in Fasten: fasten_head Unix head, but FASTQ-aware 🧬 ✅ Get first N reads (not just lines!) ✅ Works with paired-end reads ✅ Can limit by bases OR reads ✅ Blazingly fast (it's Rust 🦀) cat huge.fq | fasten_head -r 1000 Stop doing math with -n. Let the tool understand your data.
- Reposted by Tue Sparholt JørgensenCheck out this new amazing preprint by David, @tuesparholt.bsky.social , @thombooth.bsky.social, and @tilmweber.bsky.social!
- Bacterial telomeres are common, just not so much in RefSeq 'complete' genomes. But they can be added by the new tool David Faurdal wrote. I am thrilled to see this out as a preprint here: www.biorxiv.org/content/10.1... @tilmweber.bsky.social @thombooth.bsky.social
- Reposted by Tue Sparholt Jørgensen
- The telomere reconstruction software Telomore is now live here: github.com/dalofa/telom... @dalofa.bsky.social
- Reposted by Tue Sparholt JørgensenFrom genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes www.nature.com/articles/s41... 🧬🖥️🧪 github.com/HaploTeam/10...
- Reposted by Tue Sparholt JørgensenASHG Posters: The Agony and The Ecstasy #ASHG25 🧬🖥️ omicsomics.blogspot.com/2025/10/ashg...
- Reposted by Tue Sparholt Jørgensen𝘚𝘵𝘳𝘦𝘱𝘵𝘰𝘮𝘺𝘤𝘦𝘴 (and 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢🙂) aficionadas y aficionados take note 👇 ...and no, the image doesn't show reconstituted 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢 telomeres (telomores) 😉 #MicroSky
- Bacterial telomeres are common, just not so much in RefSeq 'complete' genomes. But they can be added by the new tool David Faurdal wrote. I am thrilled to see this out as a preprint here: www.biorxiv.org/content/10.1... @tilmweber.bsky.social @thombooth.bsky.social
- Bacterial telomeres are common, just not so much in RefSeq 'complete' genomes. But they can be added by the new tool David Faurdal wrote. I am thrilled to see this out as a preprint here: www.biorxiv.org/content/10.1... @tilmweber.bsky.social @thombooth.bsky.social
- The tool, Telomore, works by mapping first long then short reads to linear replicon ends, then building a consensus sequence from the reads overhanging the end, then attaching the consensus to create a complete sequence with no gaps.
- After figuring out how to attach the missing telomeres, we went on to extract replicon ends from #RefSeq to make a compendium of >2000 streptomycetaceae telomeres, clustered by sequence similarity into 137 groups with 4-300+ members.
-
View full threadthis project has been such a joy, and collaborating with dalofa.bsky.social, @thombooth.bsky.social and @tilmweber.bsky.social had been fantastic, it has been everything I ever dreamed an academic collaboration could be. Thank you guys!
- Reposted by Tue Sparholt JørgensenThe @crick.ac.uk is recruiting Early Career Group Leaders - Lab set-up, research costs, salaries for up to 5 researchers - Support for up to 12 years - Access to our core facilities - Competitive salary - Fantastic colleagues - All areas of biology Deadline 27 Nov www.crick.ac.uk/careers-stud...
- Reposted by Tue Sparholt JørgensenDear community, Bakta needs your help! To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-) (1/2)
- Reposted by Tue Sparholt JørgensenVACANCY - Independent research fellowships leading to tenured positions We’re inviting applications from outstanding researchers who either hold, or wish to apply for, Independent Research Fellowships. APPLICATION DEADLINE: 10 November 2025 Click here to apply: jic.link/Fellows
- Reposted by Tue Sparholt JørgensenRIP Jane Goodall, by all accounts a wonderful woman who loved this Far Side cartoon
- Reposted by Tue Sparholt JørgensenDelighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n
- This tool looks incredible, I've been missing something exactly like this to analyze assembly graphs, which is necessary to understand more complex genome structures.
- Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n) www.biorxiv.org/content/10.1... #Bioinformatics #genomics #assembly #assemblygraphs #software
- Reposted by Tue Sparholt JørgensenNew blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...
- Reposted by Tue Sparholt JørgensenPreprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N
- High-resolution metagenome assembly for modern long reads with myloasm biorxiv.org/content/10.1101/202…
- Reposted by Tue Sparholt JørgensenDefinitely hard to measure, but here is our best attempt from a new benchmarking paper to be preprinted in the next few weeks. Element appears to be the current king of homopolymers. Illumina does worse than HiFi beyond 20 bp. (This is all measured on human DNA)
- Reposted by Tue Sparholt JørgensenNew blog post! I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising. Check it out here: rrwick.github.io/2025/09/04/h...
- Reposted by Tue Sparholt Jørgensen🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...
- Reposted by Tue Sparholt JørgensenMaybe I am being grumpy, but can people please stop using poorly curated databases of antibiotic resistance genes (I am looking at you, DeepARG) on shotgun metagenomic data and then present these results without any reflection on their validity, or shortcomings of databases?
- Reposted by Tue Sparholt JørgensenThe TaxTriage paper www.biorxiv.org/content/10.1... has a discussion of this that I still need to grok. It's kind of mentioned as an aside in the main text, need to dig!
- Reposted by Tue Sparholt JørgensenStreptomyces venezuelae uses secreted chitinases and a designated ABC transporter to support the competitive saprophytic catabolism of chitin vs Bacillus subtilis @plosbiology.org by Anne van der Meij et al from Justin Nodwell with Marie Elliot journals.plos.org/plosbiology/...
- Reposted by Tue Sparholt JørgensenJust out: metagenomics with internal standards yields phylogenetically resolved genome ("~cell") counts of bacteria, archaea, and photosynthetic eukaryotes per L of seawater, over the AMT29 Atlantic transect, via "single copy" genes (recA, radA, psbO). Compares with microscopy and flow cytometry.
- Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes #USC_MEB #jcampubs 🌊 academic.oup.com/ismecommun/a...
- Reposted by Tue Sparholt JørgensenPreprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986
- Reposted by Tue Sparholt JørgensenA female Western Gull was recorded riding 150km in a garbage truck from San Francisco to a compost facility in Central CA, probably to forage. TWICE. An innovator, an icon, a genius. This is one of my favorite @waterbirdsociety.bsky.social papers I've ever handled as managing editor #ornithology
- The First GPS Observation of a Western Gull (Larus occidentalis) Riding in a Long-Haul Garbage Transfer Truck | doi.org/10.1675/063.... | Waterbirds | #ornithology 🪶
- Reposted by Tue Sparholt JørgensenAnnouncing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io
