Lightnews — Scholar-powered news

Reposted by Tue Sparholt Jørgensen

Stephen Turner @stephenturner.us · 7h

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

4 9

Reposted by Tue Sparholt Jørgensen

Keith Robison @omicsomics.bsky.social · 12h

ASHG Posters: The Agony and The Ecstasy

#ASHG25 🧬🖥️

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

ASHG Posters: The Agony and The Ecstasy

ASHG is a huge meeting, probably the second largest I've ever attended after ASCO. ASBMB is similar in size perhaps, though I think a hair ...

omicsomics.blogspot.com

1 2 4

Reposted by Tue Sparholt Jørgensen

STCmicrobeblog @stcmicrobeblog.bsky.social · 15h

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

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

image from https://alchetron.com/Kitasatospora

1 2 7

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 15h

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!

1

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 15h

...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.

1 1

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 15h

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)

1 1

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 15h

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.

1 1

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 15h

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.

1 1

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 15h

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.

1 1

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 15h

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.

1 2

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 15h

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.

1 2

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 15h

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

2 11 27

Reposted by Tue Sparholt Jørgensen

James Briscoe @jamesbriscoe.bsky.social · 5d

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...

Early career group leaders

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

www.crick.ac.uk

2 150 150

Reposted by Tue Sparholt Jørgensen

Oliver Schwengers @oschwengers.bsky.social · 9d

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 ;-)

(1/2)

1 18 10

Reposted by Tue Sparholt Jørgensen

John Innes Centre @johninnescentre.bsky.social · 12d

VACANCY - 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

1 27 18

Reposted by Tue Sparholt Jørgensen

James Hell Brooks @kleinman.bsky.social · 14d

RIP Jane Goodall, by all accounts a wonderful woman who loved this Far Side cartoon

27 730 3.2K

Reposted by Tue Sparholt Jørgensen

Zamin Iqbal @zaminiqbal.bsky.social · 20d

Delighted 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

14 150 300

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 28d

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.

Vijini Mallawaarachchi @vijinim.bsky.social · 28d

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

agtools: a software framework to manipulate assembly graphs

Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler to construct longer genomic f...

www.biorxiv.org

2

Reposted by Tue Sparholt Jørgensen

Heng Li @lh3lh3.bsky.social · Sep 12

New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...

2 30 56

Tue Sparholt Jørgensen @tuesparholt.bsky.social · Sep 8

I think the #illumina inc. data is also on individual reads: "To investigate correct resolution of homopolymer regions, we calculated the accuracy of the hompolymer length reported in sequenced reads" from emea.illumina.com/science/geno...
I'm looking forward to the preprint from your group!

Introducing the HP Advanced Custom Recipe for NextSeq 1000/2000 XLEAP-SBS P3 and P4 300 cycle kits

Our research teams have developed this recipe through a modification in the standard clustering protocol to improve sequencing in difficult-to-read regions. It may be of interest to users who need hig...

emea.illumina.com

1 1

Reposted by Tue Sparholt Jørgensen

Jim Shaw @jimshaw.bsky.social · Sep 7

Preprint 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

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 7

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

5 79 110

Tue Sparholt Jørgensen @tuesparholt.bsky.social · Sep 8

It's wild how different the illumina error % is between the two plots, at 15 nt homopolymer one shows 2% error and the other 20% error (phred 7 vs ca 17). Or am I missing something? bsky.app/profile/albe...

Albert Vilella, PhD. @albertvilella.bsky.social · Sep 4

Illumina publishes a new "HP homopolymer Advanced Recipe" for the NextSeq 2000 instrument line.

1

Reposted by Tue Sparholt Jørgensen

Adam Phillippy @aphillippy.bsky.social · Sep 5

Definitely 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)

2 2 6

Tue Sparholt Jørgensen @tuesparholt.bsky.social · Sep 5

True, I think six PCR cycles inside the instrument? might be different on different instruments. But PCR free libprep is still better for high and low GC regions. I randomly saw this yesterday which seems to indicate the error % for 20+ homopolymers, it might not cover 60nt bsky.app/profile/albe...

Albert Vilella, PhD. @albertvilella.bsky.social · Sep 4

Illumina publishes a new "HP homopolymer Advanced Recipe" for the NextSeq 2000 instrument line.

2

Tue Sparholt Jørgensen @tuesparholt.bsky.social · Sep 5

Thank you for the answer! Did you map the nanopore reads back to the fixed sequence to see if your nanopore data had captured them and they didn't assemble or if they were absent from the data? How long are the telomeres? I wonder why other nanopore read sets could assemble telomeres

1 1