Torsten Seemann

🃏🔀 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

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.

The 1973 edition of Google Maps. #nostalgia #Melbourne

🚀🧬 MY former colleague @micamer.bsky.social who I worked with in the early years of my career has released a BLAST service (GUI + API options) which replicates the NCBI services but with faster response times.

I'd only need white tiles for that these days 🫤

The 10-millionth job run on Galaxy Australia turned out to be my Abricate tool, which itself has been run nearly 500K times. 🤯

If only I had a dollar for every run! 😜

While browsing for a new place to rent I came across this bathroom tile design. Makes me want a pixel-art shower one day. Or a valid QR code?

Snippy: Microbial Variant Calling Community Survey Help us drive the next wave of innovation in Single-Nucleotide Polymorphism (SNP) discovery and genome analysis by sharing your valuable experiences and insights. This in-depth survey aims at understa...

🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...

Dr. Torsten Seemann and Dr. Kelsey Florek standing in front of a seated audience next to a presentation slide displaying the title "Building Resilient Public Health Genomic Systems with Data Lakes and Automation".

Big thanks to @torstenseemann.bsky.social for hosting me at the Centre for Pathogen Genomics. It was lovely to meet everyone and see the awesome binfo work happening in Asia-Pacific!

#Austrakka #Bioinformatics #PublicHealth