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
NCBI Hidden Markov Models (HMM) Release 20.0
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
Now Available! NCBI Hidden Markov Models (HMM) Release 20.0 - NCBI Insights
Download release 20.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). You can search this collection against your favorite prokaryoti...
ncbiinsights.ncbi.nlm.nih.gov
July 17, 2026 at 10:49 PM
NCBI Hidden Markov Models (HMM) Release 20.0
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
"Genome sequence data underwent quality control using FastQC [13]"
means
"We ran FastQC on all our data, but we didn't really look at, or understand the reports, and we certainly didn't remove any samples from our study."
#bioinformatiocsr #humour #reality
means
"We ran FastQC on all our data, but we didn't really look at, or understand the reports, and we certainly didn't remove any samples from our study."
#bioinformatiocsr #humour #reality
June 24, 2026 at 9:18 AM
"Genome sequence data underwent quality control using FastQC [13]"
means
"We ran FastQC on all our data, but we didn't really look at, or understand the reports, and we certainly didn't remove any samples from our study."
#bioinformatiocsr #humour #reality
means
"We ran FastQC on all our data, but we didn't really look at, or understand the reports, and we certainly didn't remove any samples from our study."
#bioinformatiocsr #humour #reality
Reposted by Torsten Seemann
For more information and to pre-register: training.galaxyproject.org/training-mat...
@galaxyproject.bsky.social @galaxytraining.bsky.social
@galaxyproject.bsky.social @galaxytraining.bsky.social
Galaxy Beyond Basics: Mastering Workflows, Automation, and Scalability
Join us for an **intensive, week-long, in-person training** designed to elevate your Galaxy expertise to new heights. This workshop is tailored for **data scientists, advanced Galaxy users, and team l...
training.galaxyproject.org
May 13, 2026 at 7:55 AM
For more information and to pre-register: training.galaxyproject.org/training-mat...
@galaxyproject.bsky.social @galaxytraining.bsky.social
@galaxyproject.bsky.social @galaxytraining.bsky.social
Excited to discover that two of my software tools (Shovill & Snippy) were used to assemble the genome of the #Hantavirus Andes Chile-9717869 strain. #bioinforbioinformatics #genomics #microbiology
www.ncbi.nlm.nih.gov/nuccore/MT95...
www.ncbi.nlm.nih.gov/nuccore/MT95...
May 11, 2026 at 8:25 AM
Excited to discover that two of my software tools (Shovill & Snippy) were used to assemble the genome of the #Hantavirus Andes Chile-9717869 strain. #bioinforbioinformatics #genomics #microbiology
www.ncbi.nlm.nih.gov/nuccore/MT95...
www.ncbi.nlm.nih.gov/nuccore/MT95...
Reposted by Torsten Seemann
Very interesting read. www.asimov.press/p/bioinforma... (Thanks to @torstenseemann.bsky.social for sharing over on the #ABACBS slack)
A Brief History of Bioinformatics Software
How computer scientists on the fringes of biology made sense of sequencing data.
www.asimov.press
April 9, 2026 at 2:59 AM
Very interesting read. www.asimov.press/p/bioinforma... (Thanks to @torstenseemann.bsky.social for sharing over on the #ABACBS slack)
Reposted by Torsten Seemann
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.
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.
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
March 29, 2026 at 2:49 PM
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.
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.
Reposted by Torsten Seemann
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...
- 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...
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....
github.com
February 27, 2026 at 1:25 PM
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...
- 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.
Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...
allthebacteria.readthedocs.io/en/latest/ov...
Overview — AllTheBacteria documentation
allthebacteria.readthedocs.io
February 27, 2026 at 7:29 AM
Joining the All-The-Bacteria project provides an annualised return on investment of 8.9% bacterial genomes.
Reposted by Torsten Seemann
@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
February 25, 2026 at 10:33 PM
@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
It was only a matter of time Google Gemini added music to its image and video offerings... gemini.google.com/app
February 21, 2026 at 11:42 PM
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...
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 🖖