On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
Three decades of biodiversity data, published one decade after we started the project!
Our new paper in @NatureComms shows how airborne eDNA from archived aerosol filters can track ecosystem changes across the tree of life—2700+ genera, weekly resolution, 34 years.
www.nature.com/articles/s41...
Excited to share our new call for papers at @asm.org's MRA journal. Do you have a database, software, or web-based tool that would be a great resource for the micro community? Consider submitting it to MRA! journals.asm.org/journal/mra/...
Our latest paper in Scientific Reports: First detection of #Sindbis #virus in wild birds in Nigeria! Screened 504 birds, found SINV RNA in African Thrushes, sequenced genome linking to Algeria, Spain & Kenya. Calls for enhanced surveillance & One Health 🦜🦟 doi.org/10.1038/s415...
Back a London Calling 10 years after my first #NanoporeConf
Not a single marine species among the 50! most studied bacteria. Gobsmacking.
Ten species comprise half of the bacteriology literature, leaving most species unstudied www.biorxiv.org/content/10.1...
Does anyone have updated benchmarks for #Dorado basecalling on different GPUs, including Apple Silicon? #Nanopore #Sequencing
Kun-peng: claims; as fast/faster than Kraken2 with the accuracy comparable to sylph! Very cool.
The design here reinforces a strong feeling I've had for a few years - moving forward in bioinfo. system-friendly & ext. memory algorithms will come to prevail. (& rust!)
www.biorxiv.org/content/10.1...
Minion Mk1D
Happy to receive a Christmas gift before the holidays #nanopore #minion #Mk1D
Source: https://www.biorxiv.org/content/10.1101/2023.12.07.570547v2.full.pdf
ganon2: up-to-date and scalable metagenomics analysis. #Metagenomics #Genomics #Bioinformatics 🧬 🖥️ @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
Sign up for next year's CBRNe Protection Symposium! A perfect opportunity to learn more about the latest in CBRNe protection research, showcase your own research. We also welcome abstract submissions for oral or poster presentation. More information here: ow.ly/g2kv50Ui2Hx
Via @FOIresearch on X
Working on designing a new hybridisation capture panel for a virus family. Previously used CATCH to select optimal set of probes but now looking for alt tools setting tiling coverage to 2 or 3 intead of complete coverage. Any recommendation of tools or code that can do it? #bioinformatics
Promotional logo for MMseqs2 16 with the MMseqs2 Rocket mascot as a smart phone like App logo
MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
Please share! Applications due Dec 15th for a starting date in Sep 2025.
Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use!
www.biorxiv.org/content/10.1...
We're looking for Reviewing Editors, over at Microbiology Resource Announcements (MRA) - call in the link below.
It's an ideal position for early-career researchers looking for a steady editing role.
#microbiology #editing #publishing #scipub #genomics #sequencing
journals.asm.org/mra/open-cal...
Spending my afternoon installing Ubuntu on my old MacBook Pro 2012. Hopefully it will be a good complement to my M3 MacBook
Modern microbiology: Embracing complexity through integration across scales
A review from @merenbey.bsky.social and Jill Banfield
www.cell.com/cell/abstrac...
I'm going to be advertising a PhD studentship (open to international students) working on long read pangenome / assembly algorithms in bacteria. Would suit someone with maths/compsci background. Aptitude and interest more important than experience. Do please spread the word. Advert to follow
Great three-part blog post by James Fellows Yates about adding software to bioconda: ubinfie.github.io/2024/08/16/a...
argnorm
Hey #AMR people,
the argNorm preprint is now available on #QUT ePrints: eprints.qut.edu.au/252448
We* designed a tool for normalizing ARG annotations across currently popular tools & dbs.
*@svetlanaup.bsky.social
Vedanth Ramji
Hui Chong
Yiqian Duan
Finlay Maguire
@luispedrocoelho.bsky.social
1/6
Happy to assist if you need help.
Did they solve your Ftul problem?
I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq
Last chance to fill in our survey! Have your say while you can :) Thanks for all those of you that already have!
Delighted to see our work on simplifying real-time analysis of nanopore reads, even without bioinformatics skills, being published! #Nanopore #Bioinformatics #plotly
academic.oup.com/bioinformati...
Lets start the scientific evaluation of different Semla buns
A metagenomic alpha-diversity index for microbial functional biodiversity academic.oup.com/femsec/artic... #jcampubs
Md. Hasin Abrar and I recently posted a pre-print "PLA-complexity of k-mer multisets" We explore a measure of a k-mer multiset complexity, first suggested by Boffa et al, which we call the PLA-complexity.
doi.org/10.1101/2024...
(1/n)
MultiQC is swapping to use plotly for generating plots.
seqera.io/blog/multiqc...
