Tue Sparholt Jørgensen
@tuesparholt.bsky.social
Pinned
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
“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
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
November 13, 2025 at 10:09 AM
“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
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
Reposted by Tue Sparholt Jørgensen
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
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
October 24, 2025 at 1:53 PM
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
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
Reposted by Tue Sparholt Jørgensen
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...
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...
embl.wd103.myworkdayjobs.com
October 10, 2025 at 7:30 AM
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...
Reposted by Tue Sparholt Jørgensen
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...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 8:16 PM
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...
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.
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.
October 21, 2025 at 12:13 AM
🚀 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.
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 Jørgensen
Check 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
October 20, 2025 at 8:14 AM
Check out this new amazing preprint by David, @tuesparholt.bsky.social , @thombooth.bsky.social, and @tilmweber.bsky.social!
Reposted by Tue Sparholt Jørgensen
The telomere reconstruction software Telomore is now live here: github.com/dalofa/telom... @dalofa.bsky.social
GitHub - dalofa/telomore: Gotta find them telomeres
Gotta find them telomeres. Contribute to dalofa/telomore development by creating an account on GitHub.
github.com
October 16, 2025 at 8:20 AM
The telomere reconstruction software Telomore is now live here: github.com/dalofa/telom... @dalofa.bsky.social
Reposted by Tue Sparholt Jørgensen
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes www.nature.com/articles/s41... 🧬🖥️🧪 github.com/HaploTeam/10...
October 15, 2025 at 5:55 PM
From 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 Jørgensen
Reposted by Tue Sparholt Jørgensen
𝘚𝘵𝘳𝘦𝘱𝘵𝘰𝘮𝘺𝘤𝘦𝘴 (and 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢🙂) aficionadas y aficionados take note 👇
...and no, the image doesn't show reconstituted 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢 telomeres (telomores) 😉
#MicroSky
...and no, the image doesn't show reconstituted 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢 telomeres (telomores) 😉
#MicroSky
October 15, 2025 at 10:17 AM
𝘚𝘵𝘳𝘦𝘱𝘵𝘰𝘮𝘺𝘤𝘦𝘴 (and 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢🙂) aficionadas y aficionados take note 👇
...and no, the image doesn't show reconstituted 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢 telomeres (telomores) 😉
#MicroSky
...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
October 15, 2025 at 10:04 AM
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 @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...
- 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
October 10, 2025 at 8:20 AM
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...
- 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 Jørgensen
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)
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)
October 6, 2025 at 7:27 AM
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)
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 Jørgensen
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
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
October 3, 2025 at 3:11 PM
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
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 Jørgensen
RIP Jane Goodall, by all accounts a wonderful woman who loved this Far Side cartoon
October 1, 2025 at 6:09 PM
RIP Jane Goodall, by all accounts a wonderful woman who loved this Far Side cartoon
Reposted by Tue Sparholt Jørgensen
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
Thread 1/n
September 25, 2025 at 9:29 PM
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
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
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
September 17, 2025 at 8:59 AM
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.
Reposted by Tue Sparholt Jørgensen
New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...
lh3.github.io/2025/09/11/a...
September 12, 2025 at 3:26 AM
New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...
lh3.github.io/2025/09/11/a...
Reposted by Tue Sparholt Jørgensen
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
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 https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
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
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
Reposted by Tue Sparholt Jørgensen
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)
September 5, 2025 at 12:55 PM
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)
Reposted by Tue Sparholt Jørgensen
New 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...
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...
Cross-sample homopolymer polishing with Pypolca
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
September 4, 2025 at 6:37 AM
New 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...
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...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 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...
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 Jørgensen
Maybe 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?
August 20, 2025 at 10:27 AM
Maybe 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 Jørgensen
The 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!
TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection
Motivation TaxTriage is a comprehensive pathogen identification workflow designed for both short– and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de n...
www.biorxiv.org
August 20, 2025 at 4:15 PM
The 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!