Samuel Lampa

Release SeqKit v2.13.0 (10-year-old birthday version) · shenwei356/seqkit Changelog SeqKit is 10 years old! SeqKit v2.13.0 - 2026-02-28 seqkit: add support for reading and writing LZ4 compression format. new command: seqkit sample2: improved seqkit sample by @stahiga....

Can't wait to release a 10-year-old birthday version for SeqKit!

- 10 years
- 2 papers, 3500 citations
- 20 contributors
- 40 subcommands
- 880 commits
- 500 issues
- 685.5K Bioconda total downloads

Thank you all, dear contributors and users!
I'll keep maintaining it.

github.com/shenwei356/s...

BioAIrepo: EMBL-EBI’s hub for life science AI models New EMBL-EBI repository helps researchers share and reuse machine learning models trained on life science data.

📢 We want your feedback on our new pilot project for sharing AI models in life science research.

Finding, reusing and citing machine learning models remains a major challenge in the life sciences.

BioAIrepo is here to help.

www.ebi.ac.uk/about/news/t...

SeqKit is the best!! Such a joy to use for all kinds of messing around with sequences. The thought and attention to detail that went into it is impressive to say the least. Huge congrats on the 10 year anniversary! 🙌🎉😎

Snakemake Hackathon March 2026 We are excited to announce the Snakemake Hackathon 2026, to be held 9-13 March, 2026 at the Technical University Munich. This event will bring together passionate developers and data scientists to col...

Want to help shaping the future of #Snakemake? Then participate in the Snakemake hackathon 2026 in Munich! There's still room as the maximum number of participants is not yet reached. You can register here: indico.cern.ch/e/snakemake-...

#sciworkflows #reproducibility

Better workflow graph (more compact for long commands and paths by auto-folding), coming up in the next release of #scicommander ... #sciworkflows

Interesting!

Scrappy San Diego startup goes toe-to-toe with gene-sequencing giant Illumina Element Biosciences created a high-throughput benchtop device that can deliver a whole genome for $100 – half the price of Illumina’s technology.

Thank you to Noelle Harff of The San Diego Union Tribune for covering the launch of VITARI™, the first ever high-throughput sequencing system that can deliver a $100 high-quality whole genome on the benchtop at scale.

Read the full article: https://bit.ly/4aSZMEr.

#BiotechInnovation #Multiomics

Detecting foldback artifacts in long-reads - BMC Genomics Long-read sequencing data is useful for detecting large and complex structural variations; however, technical artifacts can lead to false structural variant calls. In our analyses, we became aware of ...

Our paper on foldback artifacts in long-read sequencing is now published in BMC Genomics!

We introduce Breakinator to flag foldback and chimeric artifacts across library types, sequencers, and chemistries.

Paper: link.springer.com/article/10.1...

With Matthew Meyerson and @lh3lh3.bsky.social

Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis AbstractMotivation. Long-read sequencing (LRS) is increasingly used for human medical research and clinical diagnostics, due to its capacity to generate co

Say hello to Nallo - our Nextflow pipeline for long-read WGS analysis!👋 It handles both ONT and PacBio data and we’re using this for rare disease and population projects in Sweden. A big team effort by Felix Lenner, Anders Jemt et al.🧬💻 academic.oup.com/bioinformati...

Were you aware that these are available for the community:
- an efficient fasta/q parser in Rust
- a quick rolling hash library
- a minimizer library
All in Rust 🦀

#TEsky

MAX: A high-performance inference framework for AI MAX provides powerful libraries and tools to develop, optimize and deploy AI on GPUs fast. Get incredible performance, hardware portability, and complete control over every layer of the stack.

With #RAMmageddon upon us I think we really need to start working smarter, not just pouring more hardware at problems.

That's one reason I believe platforms like Modular's MAX will only grow in importance, by enabling more innovation in the AI stack. www.modular.com/max

Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁

A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species - Genome Biology Background The role of transposable elements (TEs) in host adaptation has gained interest in recent years. Individuals of the same species undergo independent TE insertions, providing genetic variabil...

🚨📢📄 Article in press in Genome Biology doi.org/10.1186/s130...
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇

Pathways, outputs and impact of NIH-supported bioinformatics and genomics graduate trainees in Africa Abstract. Global biomedical and health research is increasingly relying on genomic and computational approaches, largely driven by the increasing volumes o

From #OUP 's #Briefings in Bioinformatics journal | Pathways, outputs and impact of #NIH -supported #bioinformatics & #genomics graduate trainees in #Africa | #Education #OpenScience #H3ABionet #H3Africa 🧬 🖥️ 🧪 🔓
⬇️
academic.oup.com/bib/article/...

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)

GitHub - RagnarGrootKoerkamp/oxford-bioinformatics-template: Improved version of the Oxford Bioinformatics paper template Improved version of the Oxford Bioinformatics paper template - RagnarGrootKoerkamp/oxford-bioinformatics-template

Community service:
Updated the oxford-bioinformatics template repo because apparently the template changed again, and it's still the top google hit, and figuring out the right parameters remains messy, and they are still inconsistent.

github.com/RagnarGrootK...

Sleep and Biological Rhythms Small shifts in diurnal rhythms are associated with an increase in suicide: The effect of daylight saving Michael BERK, Seetal DODD, Karen HALLAM, Lesley BERK, John GLEESON, Margaret HENRY 21 February 2008 Abstract Large disruptions of chronobiological rhythms are documented as destabilizing individuals with bipolar disorder; however, the impact of small phase altering events is unclear. Australian suicide data from 1971 to 2001 were assessed to determine the impact on the number of suicides of a 1-h time shift due to daylight saving. The results confirm that male suicide rates rise in the weeks following the commencement of daylight saving, compared to the weeks following the return to eastern standard time and for the rest of the year.

“Suicides rise following commencement of Daylight Saving Time, compared to the return to Standard Time.”

Graphic with a blue 3D chromosome on the left and text on the right: “Group Leaders in Data Science and AI for Molecular and Health Data.” Logos of University of Helsinki, FIMM, and HiLIFE. “Apply by 15 March.”

We're recruiting 1-2 Group Leaders in Data Science and AI for Molecular & Health Data!
Candidates with strong background in ML/AI/data science and interest in applying analytical methods to large-scale molecular and health data are particularly encouraged to apply:
🔗 jobs.helsinki.fi/job/Helsinki...

🚨 The final version is out: how transposons help keep our hearts beating ❤️
Proud of this one with @1995dana.bsky.social, huge thanks to @trono-lab.bsky.social.
Give it a read! #TEsky

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

1. The thing about science that these jokers don't understand is that science cannot be vibe-coded.

Whatever its flaws, the point with vibe coding is that you're trying to quickly make something that sorta works, where you can immediately sorta see if it sorta works and then sorta use it.

Using gen AI means sacrificing accuracy for convenience. Its purpose is to cut corners. If that’s how you roll, science has no need for you.

Vacancy card with a rod-shaped microbe as background image that reads "Research Scientist. To create and use a transposon mutant library in Salmonella and build tools for transposon mutagenesis in higher organisms. Salary £37,500 to £45,350. Contract length 2 years. Apply by 28 January 2026.

⏰ Closing soon! The Webber group is looking for a Research Scientist to use high throughput transposon mutagenesis to help understand mechanisms of action, host susceptibility and resistance to antimicrobials.

💷 £37,500 to £45,350
🗓️ Apply by 28 January 2026
➡️ buff.ly/8iXH22u

I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻

Please repost

Apply here: www.wur.nl/en/vacancy/p...

A holocentric pangenome links karyotype evolution to meiotic recombination https://www.biorxiv.org/content/10.64898/2026.01.17.700048v1

Asking google who is more suave, Ian Dunt or Dorian Lynskey, with -noai in the search term, returns no hits

Asking google who is more suave, Ian Dunt or Dorian Lynskey, returns some AI blather

In case useful @iandunt.bsky.social , @soniaz.bsky.social has just shown me how to turn off the AI summary in google search! Just add -noai. Just did a simple test comparing you and @dorianlynskey.bsky.social

I can’t help thinking how Barbara McClintock would have responded to papers like this. I mean, beyond, I TOLD YOU!

Many thanks to the folks who responded to my #TEsky query about transposable elements. Wow, what an amazing field that’s become.

For those of us interested in software development, data structure design etc in science, this is a must-read. A taste of what is happening in communities letting AI agents go wild writing code, creating PRs, writing documentation : spoiler - humans get addicted, lose perspective, slop everywhere.