"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

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)

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.

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

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...

💾 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...

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...

💾 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 🖖

🚨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.

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?

🦘✂️ 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...

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

Want to help build capacity public health pathogen bioinformatics in the Asia Pacific region? 🦘 Based in Melbourne Australia with me ✈️ Travel to and work internationally 🧠 Lead strategy, training & infrastructure Applications close soon! jobs.unimelb.edu.au/caw/en/job/9...

Don't know who to follow for the best in microbial bioinformatics? This is the Starter Pack you need! bsky.app/starter-pack...

Really hoping there isn't a Y2.25K bug we missed.

When blue screens were what made kids dream.

Love this poster on the Mandelbrot Set

🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀 Check it out here: doi.org/10.1101/2024... And find the code here: github.com/mbhall88/lrge 🧵👇

I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io

I nominate this for #bioinformatiocs tool name of the year. I love it when Aussie home grown software have some "Australiana" in them! 🇦🇺 github.com/AroneyS/binc...

Today I discovered that there is a street near my house named "Nullarbor Pl". I could take my laptop down there and run "nullabor.pl" at Nullarbor Pl. #coincidence