A Brief History of Bioinformatics Software How computer scientists on the fringes of biology made sense of sequencing data.

Very interesting read. www.asimov.press/p/bioinforma... (Thanks to @torstenseemann.bsky.social for sharing over on the #ABACBS slack)

Genomic epidemiology of Salmonella and Campylobacter in poultry production: Quantifying the contribution of primary breeders | PNAS The US broiler production system processes over 9.3 billion chickens annually through a highly integrated pyramid structure where two primary breed...

www.pnas.org/doi/10.1073/...
If you ever need lto be convinced by how bad the "Contributed by" track is at @pnas.org ...

Only author: David Lipman, handling editor: David Lipman. Only integrity-free person not embarrassed by such a paper: David Lipman.

Even uses "I did" in the abstract. Shameful.

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...

Joining the All-The-Bacteria project provides an annualised return on investment of 8.9% bacterial genomes.

@wytamma.bsky.social 's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n

‎Gemini - direct access to Google AI Created with Gemini

I used it to create a microbial bioinformatics G-Funk 90's rap snippet 😆

gemini.google.com/share/1df0e1...

It was only a matter of time Google Gemini added music to its image and video offerings... gemini.google.com/app

Patrick / coffeestains · GitLab This package provides an essential feature to LaTeX that has been missing for too long. It adds a coffee stain to your documents. A lot of time can...

A LaTeX package to add coffee strains to your documents😆
framagit.org/Pathe/coffee...

Patrick / coffeestains · GitLab This package provides an essential feature to LaTeX that has been missing for too long. It adds a coffee stain to your documents. A lot of time can...

framagit.org/Pathe/coffee...

🃏🔀 Let me shuffle that deck of cards for you!

printf "%s\n" {2,3,4,5,6,7,8,9,10,J,Q,K,A}{♠,♥,♦,♣} | shuf | xargs -n 9

K♣ 5♣ 6♠ 4♠ 3♦ J♦ 7♦ 8♣ 9♠
2♠ 9♥ J♥ 9♣ 10♠ J♣ Q♥ 7♠ Q♠
6♥ A♠ 8♠ 10♥ K♥ 10♦ 4♣ A♣ A♥
5♦ 5♥ 6♣ J♠ Q♣ A♦ 3♣ 4♥ 3♠
4♦ 3♥ K♠ 7♥ 6♦ 8♦ 7♣ K♦ 8♥
9♦ 2♥ 5♠ 10♣ Q♦ 2♦ 2♣

Intro to R for Biologists Ever wanted to visualise your own data? You can with R!

"Intro to R for Biologists" – Learn to visualise biological data with R!

Led by Jessica Chung (Melbourne Bioinformatics), this free in-person workshop on 24 February at 21 Bedford St, North Melbourne covers loading data, creating plots with ggplot, and working with RNA-seq data using tidyverse.

GitHub - ebiggers/libdeflate: Heavily optimized library for DEFLATE/zlib/gzip compression and decompression Heavily optimized library for DEFLATE/zlib/gzip compression and decompression - ebiggers/libdeflate

🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.

libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix

github.com/ebiggers/lib...

Although the idea is cool, for the case of {ATGC} alphabet and match=1 mismatch=0, it would probably slow it down. But I am planning to include support for larger IUPAC alphabet which has more complex scoring, so your method would be more efficient. FIled at github.com/tseemann/snp... - thanks!

No I don't do that; but it's a very cool approach, esp as the index will fit in cache. I am using multi-threading across rows, and using SIMD vector instructions columns (16 to 32 sites per CPU instruction. I'll make an issue to compare these methods!

It takes a multiple sequence alignment, usually a set of pseudomolecules from a snp calling pipeline against a reference

Release Go the distance even faster · tseemann/snp-dists Speed major fix to CPU parallelisation - far better scaling -x maxdiff option to short-circuit distant pairs -L option to only calculate the lower triangle of the matrix (2x faster) Features -t ...

💾 snp-dists 1.2.0

Major upgrade to this distance matrix tool - huge performance gains from multithreading (-j), max distance short circuiting (-x) and lower triangle output (-L).

#bioinformatiocs #microbiology #genomics
github.com/tseemann/snp...

Release Next time I'll try to be FASTA · tseemann/any2fasta New features Option -k is keep processing even when some inputs fail option -g to include GBK version suffix option s to strip desc from>id desc in ID lines Support for PDB protein structure forma...

💾 any2fasta 0.8.1 is released!

The FASTA format is now 40 years old (Pearson & Lipman) and any2fasta makes it easy for your scripts and pipelines that accept FASTA to also accept other formats, even if compressed! eg. .gbk.gz

#bioinformatiocs #microbiology #genomcs
github.com/tseemann/any...

This is why @wytamma.bsky.social and I have been writing SNIPPY-NG ! It will support short reads, long reads, and assemblies as inputs. You can check it out at github.com/centre-patho...

It's not ready for prime-time yet, but it's useable!

Happy Bioinformatics Xmas!
The annual celebration of the unknown amino acid.
#bioinformatiocs #humour

Releases · tseemann/mlst :id: Scan contig files against PubMLST typing schemes - tseemann/mlst

💾 mlst 2.25.0 has been released!

Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases.
#bioinformatiocs #microbiology #genomics

github.com/tseemann/mls...

There is no such thing as tenure in Australia unfortunately. I still have to find my own salary. I'm hoping my 9th attempt for a NHMRC fellowship will succeed, results in Feb 2026. #australia #academia

💾 Prokka 1.15.6 is released!

This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics

github.com/tseemann/pro...

Releases · tseemann/shovill ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill

💾 Shovill 1.4.1 has been released!
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...

Great to visit Melbourne & speak at the Doherty Institute yesterday, hosted by the newly crowned King Professor @torstenseemann.bsky.social . So many great microbial genomics folk out here; today at Monash, seeing @yekwah.bsky.social @kelwyres.bsky.social and co. So much great science+great students

Releases · tseemann/abricate :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate

💾 ABRicate 1.2.0 has been released!

This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics

github.com/tseemann/abr...

This poster design was the hard work of @wytamma.bsky.social who is implementing Snippy-NG. You should follow him now - an amazing ECR who produces a lot of very cool stuff.

It's not just because @torstenseemann.bsky.social is a bioinformatics legend but this may be my favourite #abacbs2025 poster because I'm a #trek tragic 🖖

Registration and abstract submission for MicroSeq2025 is open. Abstract submission closes August 8, 2025. Participants can register at microseqconference.com. MicroSeq2025 is an online meeting being held on September 3rd and 4th, focused on research being conducted on sequencing data generated from microbiological samples (bacteria, fungi, and viruses). MicroSeq2025 is supported by The Australian Society for Microbiology, the Australasian Virology Society, and Microbial Genomics.

🚨Abstract submission & registration for #MicroSeq2025 is OPEN! 🚨Get in quick! The first 50 registrations are FREE for PhD students and ECRs who are current ASM members, thanks to @aussocmic.bsky.social.

Head to our website to register now 👇
www.microseqconference.com/registration...

Google Slides has a new "Stock images" option when you "Insert Image" - you get these two options for the search term #bioinfortmics ...

🚀 Pushed some updates to taxonomy.onecodex.com

- Example queries to help you get started
- Summary section for easier interpretation
- Perf. improvements