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

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

"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

For more information and to pre-register: training.galaxyproject.org/training-mat... @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

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...

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.

asimov.press

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.

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...

pnas.org

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...

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

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

Zamin Iqbal@zaminiqbal.bsky.social · 5mo ago

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...

@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

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

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

🃏🔀 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.

Intro to R for Biologists

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

eventbrite.com

🗜️⚡ 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...

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

💾 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 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

💾 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...

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

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...

Releases · tseemann/mlst

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

github.com

💾 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...

Releases · tseemann/shovill

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

github.com

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...

Releases · tseemann/abricate

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

github.com

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.

Jovana Maksimovic@jovmaksimovic.bsky.social · 8mo ago

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 🖖

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 🖖

🚨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.