Tue Sparholt Jørgensen

GitHub - lh3/human-asm: A collection of high-quality human genomes A collection of high-quality human genomes. Contribute to lh3/human-asm development by creating an account on GitHub.

579 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

Life Identification Numbers: A bacterial strain nomenclature approach Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

Huge 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 👇

An archaeal genetic code with all TAG codons as pyrrolysine Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...

✨ 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...

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot 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/...

Genome integrity relies on rapid recycling of DNA Pol III in bacteria | PNAS DNA replication requires precise coordination between DNA unwinding and DNA synthesis. In all domains of life, protein–protein interactions at the ...

Happy 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!

Logo of Bin Chicken (Australian white ibis) on a rubbish bin, pulling out a strand of DNA

“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

link to the article to avoid 10000 cookies: elifesciences.org/reviewed-pre...

Did 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

Staff Scientist About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

I 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...

Around 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...

🚀 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.

Check out this new amazing preprint by David, @tuesparholt.bsky.social , @thombooth.bsky.social, and @tilmweber.bsky.social!

hahaha this is amazing!!!

The telomere reconstruction software Telomore is now live here: github.com/dalofa/telom... @dalofa.bsky.social

From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes www.nature.com/articles/s41... 🧬🖥️🧪 github.com/HaploTeam/10...

ASHG Posters: The Agony and The Ecstasy

#ASHG25 🧬🖥️

omicsomics.blogspot.com/2025/10/ashg...

𝘚𝘵𝘳𝘦𝘱𝘵𝘰𝘮𝘺𝘤𝘦𝘴 (and 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢🙂) aficionadas y aficionados take note 👇

...and no, the image doesn't show reconstituted 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢 telomeres (telomores) 😉
#MicroSky

this 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!

...an information which David then used to beautifully show that the protein folds similarly in structure but not in sequence to the known telomere maintenance systems main DNAbinding domain.

Then @thombooth.bsky.social used the presence/absence of known telomere proteins to identify a potentially new telomere protein which is linked to the Sg2247 class telomere, which previously did not have an identified maintenance system (notice the dot in the red circle)

David then analyzed the end replication proteins and could identify a known system in 76% of strains. Extremely interestingly, he used that to show that certain telomere sequences are linked to specific telomere maintenance proteins.

To our knowledge, the >2000 telomeres which were clustered into 137 groups is the first large scale attempt at dissecting the diversity of the telomeres of streptomyces, and allow us to make additional discoveries, like the potentially #plasmid specific AGA telomere.

We noticed that quite few of the RefSeq genomes had replicon ends which clustered as telomeres, and decided to quantify it: while only 15% of RefSeq 'complete' chromosomes were found to have both telomeres, 78% of Telomore completed chromosomes had both telomeres.

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.

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.

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

Early career group leaders We appoint researchers from across biology and biomedicine to set up their first groups at the Crick.

The @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...

Dear 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 ;-)

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