Amanda Clare

Taming the reference genome jungle: the refget sequence collection standard. #ReferenceGenomes #Transcriptomes #SequenceCollectionStandards #GA4GH @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...

🌱 Tomorrow we launch Plant Science Wales at the National Botanic Garden of Wales!

Explore seed banks, herbarium tours & panels on agri-tech, biophilia & more.

Organised by IBERS & NBGW, supported by the Learned Society of Wales. Follow for behind-the-scenes & speaker highlights!

🚀 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.

New blogpost on my concerns about Wellcome LEAP new $50m program on autism/microbiome links. deevybee.blogspot.com/2025/10/a-le...
#autism #microbiome #biomarkers #diagnostic

La créatrice du programme d’échange Erasmus, Sofia Corradi, est morte Quelque 16 millions de jeunes ont pu étudier dans d’autres pays d’Europe grâce au projet lancé en 1987 par cette professeure italienne qui s’est éteinte à l’âge de 91 ans.

La créatrice du programme d’échange Erasmus, Sofia Corradi, est morte

Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#

New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Burrows-Wheeler Indexing - YouTube Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.

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)

Independent research fellowships leading to tenured positions at the John Innes Centre.

Repost = nice. Thank you very much!!!

✨ September 29, 2025 will be recorded as the zenith of the Peak of Inflated Expectations ✨ www.microsoft.com/en-us/micros...

Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies Abstract. Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynCom

The main work from my time in Aachen is now out 🎉 if you have wanted to make a SynCom that captures the functional-landscape of microbiota, MiMiC2 makes that possible based on metagenomic data! 1/7 doi.org/10.1093/isme...

We are glad to announce that the next workshop “Data Structures in Bioinformatics” (DSB 2026) will take place in Venice, Italy, on *February 18-19*, 2026. dsb-meeting.github.io/DSB2026/ Book the dates! #DSB26

A play in two parts.

#Aberystwyth

Science is the ultimate team sport! Next week @qubelfastofficial.bsky.social hosts researchers from 15 countries for the EU H2020 HoloRuminant project. International collaboration, different perspectives, shared data, common goals! 🌍🐄 Looking forward to it!
#HoloRuminant #MicrobialEcology #EUH2020

Research Associate in Computational Genomics Position Details Fixed Term for five years I Full Time Academic Level A | $88,842 - $107,666 pa plus 17% Super Location: Bedford Park / Kaurna Country / Australia View Position Description About the R...

Position 2:

Research Associate in Computational Genomics
Design and implement high-performance workflows integrating GPU programming, deep learning, and large-scale data integration
flinders.wd3.myworkdayjobs.com/en-US/flinde...

AllTheBacteria - all bacterial genomes assembled, available and searchable The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...

An evergreen thread: Race/Ethnicity is *not the same* as genetics, and you can't use Race/Ethnicity as a sort of stand-in for genetics. These two concepts are connected via aspects like skin colour, but the connection is alot less profound and categorical than most people think.

An old image of a salivary gland chromosome from Drosophila melanogaster, with lines across different segments indicating contact points.

The original circos plot? From the 1947-1948 Carnegie Yearbook, the page prior to McClintock's Mutable Loci in Maize paper.

Gene Fetch: A Python tool for sequence retrieval from GenBank across the tree of life Parsons et al., (2025). Gene Fetch: A Python tool for sequence retrieval from GenBank across the tree of life. Journal of Open Source Software, 10(112), 8456, https://doi.org/10.21105/joss.08456

New genbank data retrieval tool just dropped, through one of my favorite journals, JOSS. This one focuses on retrieving taxonomically targeted coding sequences, with hard coded support for your common barcoding targets. Could be a fun tool for classes too. 💻🧬

joss.theoj.org/papers/10.21...

Research Fellow - ABC12486 | Aberdeen City Council | myjobscotland View details and apply for this research (further / higher education) role in Aberdeen with Aberdeen City Council on myjobscotland

Our NIHR Health Determinants Research Collaborative is hiring a Research Fellow

£45-51k

We're a well-funded collaboration between local authority, university & NHS working to have a measureable impact on public health. I'm happy to chat with anyone interested!

myjobscotland.gov.uk/councils/abe...

Measuring scientific impact beyond academia: An assessment of existing impact metrics and proposed improvements How does scientific research affect the world around us? Being able to answer this question is of great importance in order to appropriately channel efforts and resources in science. The impact by sci...

We compared citations with REF impact from the 2014 data and it did not correlate. journals.plos.org/plosone/arti...

Microbial Databases, Software Tools, and Web Services Publish your microbial database or software tool in MRA to gain recognition, citations, and community trust.

Over at Microbiology Resource Announcements (an @asm.org journal) we'd like to be publishing more public databases and tools, including short open source software announcements. We even have a call out!

We hope you might conisder us for your work (more in link).

journals.asm.org/journal/mra/...

Coming to a coastline near you soon.

This is great 🙌🙏 Martin Robbins on the tyranny of small numbers.

OReO: optimizing read order for practical compression AbstractMotivation. Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and mana

Paper alert!
We present Oreo a tools that reorder long reads datasets in a way to compress them efficiently with ANY universal compressor like gz, zstd, xz ...
TLDR: You can get state of the art compression WITHOUT a dedicated compressor/decompressor!
academic.oup.com/bioinformati...
A thread!

🌊 Algal Revolution is coming to the @royalsociety.org Summer Science Exhibition! 🧪

IBERS’ Jessica Adams, PhD students Luke Barnett & Jenny Griffiths, and a team of volunteers will be sharing the wonders of algae in London, 1–6 July!

#AlgalRevolution #RoyalSociety #ScienceOutreach

Swansea University graduate applied for 646 roles before getting a job Caitlin Morgan doubted if her degree was worth it as competition for graduate jobs hit record high.

'She said initially her CV was not written in a way that could be read by a resume screening programme called ATS (applicant tracking system), where AI reads CVs.' Talking to finalists, the use of AI to screen was a huge frustration for them. Talking to employers, use of AI by applicants was ditto.

Excited to introduce LiftOn – an open-source tool for accurate, scalable liftover of genome annotations (GFF) across assemblies. 🚀

👉 Code & community: github.com/Kuanhao-Chao...

It’s been incredibly rewarding building this for the genomics community. Can’t wait for your feedback and contributions!

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...