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
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
A LaTeX package to add coffee strains to your documents😆
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" – 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.
🗜️⚡ 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
💾 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...
💾 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
💾 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...
💾 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
💾 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
You might be wondering why we haven't updated outbreak.info for months.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
On more than one occasion I've thought of a cool idea for a bioinformatics program only to realize @torstenseemann.bsky.social already wrote it a decade ago.
