Torsten Seemann
@torstenseemann.bsky.social
Professor @ University of Melbourne, Australia
Microbial bioinformatics, genomics, software, clinical and public health microbiology
https://tseemann.github.io
Microbial bioinformatics, genomics, software, clinical and public health microbiology
https://tseemann.github.io
Pinned
A LaTeX package to add coffee strains to your documents😆
framagit.org/Pathe/coffee...
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
February 9, 2026 at 5:31 AM
A LaTeX package to add coffee strains to your documents😆
framagit.org/Pathe/coffee...
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♣
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♣
January 21, 2026 at 6:15 AM
🃏🔀 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♣
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♣
Reposted by Torsten Seemann
"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.
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.
Intro to R for Biologists
Ever wanted to visualise your own data? You can with R!
www.eventbrite.com
January 20, 2026 at 11:02 PM
"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.
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...
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
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
github.com
January 20, 2026 at 1:37 AM
🗜️⚡ 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...
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
💾 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...
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 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 ...
github.com
December 31, 2025 at 1:58 AM
💾 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...
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...
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...
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...
github.com
December 30, 2025 at 5:16 AM
💾 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...
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...
December 25, 2025 at 12:31 AM
💾 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...
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...
Releases · tseemann/mlst
:id: Scan contig files against PubMLST typing schemes - tseemann/mlst
github.com
December 22, 2025 at 9:15 PM
💾 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...
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...
💾 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...
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...
Release Heading into the sunset · tseemann/prokka
The future
This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
github.com
December 15, 2025 at 9:09 PM
💾 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...
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...
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...
Releases · tseemann/shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill
github.com
December 13, 2025 at 9:15 PM
💾 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...
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...
Reposted by Torsten Seemann
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
December 4, 2025 at 7:33 AM
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 '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...
Releases · tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate
github.com
December 5, 2025 at 11:27 PM
💾 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 '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 🖖
December 4, 2025 at 1:42 AM
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.
Reposted by Torsten Seemann
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 🖖
November 26, 2025 at 12:34 AM
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 🖖
Reposted by Torsten Seemann
🚨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...
Head to our website to register now 👇
www.microseqconference.com/registration...
July 21, 2025 at 2:16 AM
🚨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...
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 ...
June 25, 2025 at 11:09 PM
Google Slides has a new "Stock images" option when you "Insert Image" - you get these two options for the search term #bioinfortmics ...
Reposted by Torsten Seemann
🚀 Pushed some updates to taxonomy.onecodex.com
- Example queries to help you get started
- Summary section for easier interpretation
- Perf. improvements
- Example queries to help you get started
- Summary section for easier interpretation
- Perf. improvements
Taxonomy Time Machine
Explore and compare the history of the NCBI Taxonomy Database. Instantly browse, search, and reconstruct taxonomic lineages at any point in time. Open source, web-based, and API-accessible.
taxonomy.onecodex.com
May 24, 2025 at 9:38 PM
🚀 Pushed some updates to taxonomy.onecodex.com
- Example queries to help you get started
- Summary section for easier interpretation
- Perf. improvements
- Example queries to help you get started
- Summary section for easier interpretation
- Perf. improvements
Reposted by Torsten Seemann
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.
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.
May 28, 2025 at 11:02 PM
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.
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.
Reposted by Torsten Seemann
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.
April 14, 2025 at 4:53 AM
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
March 14, 2025 at 3:38 AM
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.
We would love feedback on a new NCBI-BLAST service we are launching today: sky-blast.com
Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable
Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable
March 12, 2025 at 1:19 AM
🚀🧬 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.
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! 😜
If only I had a dollar for every run! 😜
Which locally-developed bioinformatics tool was used to run Galaxy Australia’s 10 millionth job? It has been used to screen for antimicrobial resistance and virulence genes in 490,507 jobs run on #GalaxyAustralia so far! Clue: @torstenseemann.bsky.social www.biocommons.org.au/news/10m-jobs
Galaxy Australia’s 10 millionth job relied on popular locally-developed tool — Australian BioCommons
The ten millionth job completed on the Galaxy Australia service analysed pathogen samples for known antibiotic resistance genes using the ABRicate tool. You’d be surprised how many time this Australia...
www.biocommons.org.au
March 10, 2025 at 7:59 AM
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! 😜
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?
March 10, 2025 at 7:53 AM
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?
🦘✂️ 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...
forms.gle/YJP6WQjsk8KK...
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...
forms.gle
March 4, 2025 at 9:04 AM
🦘✂️ 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...
forms.gle/YJP6WQjsk8KK...