Andreas Sjödin

Microbial Databases, Software Tools, and Web Services Publish your microbial database or software tool in MRA to gain recognition, citations, and community trust.

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/...

First detection of Sindbis virus in wild birds in Nigeria - Scientific Reports Scientific Reports - First detection of Sindbis virus in wild birds in Nigeria

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: an ultra-memory-efficient, fast, and accurate pan-domain taxonomic classifier for all Comprehensive metagenomic sequence classification of diverse environmental samples faces significant computing memory challenges due to exponentially expanding genome databases. Here, we present Kun-p...

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.

AllTheBacteria - all bacterial genomes assembled, available and searchable The bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either unassemb...

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...

Microbiology Resource Announcements Open Call for Reviewing Editors Microbiology Resource Announcements is looking for microbiologists with expertise in genome sequencing to join our Board of Reviewing Editors.

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 This review explores the history of microbiology and contemplates the future of this evolving discipline as microbiologists embrace rapidly emerging technologies to explore systems of great complexity...

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?

Genomics+Bioinformatics Starter Pack 🧬🖥️ Join the conversation

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!

Nanometa live: a user-friendly application for real-time metagenomic data analysis and pathogen identification AbstractSummary. Nanometa Live presents a user-friendly interface designed for real-time metagenomic data analysis and pathogen identification utilizing Oxford

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

PLA-complexity of k-mer multisets bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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: A fresh coat of paint | Seqera New graphs made with Plotly come to MultiQC.

MultiQC is swapping to use plotly for generating plots.
seqera.io/blog/multiqc...

Estimating Fold Changes from Partially Observed Outcomes with Applications in Microbial Metagenomics We consider the problem of estimating fold-changes in the expected value of a multivariate outcome that is observed subject to unknown sample-specific and category-specific perturbations. We are motivated by high-throughput sequencing studies of the abundance of microbial taxa, in which microbes are systematically over- and under-detected relative to their true abundances. Our log-linear model admits a partially identifiable estimand, and we establish full identifiability by imposing interpretable parameter constraints. To reduce bias and guarantee the existence of parameter estimates in the presence of sparse observations, we apply an asymptotically negligible and constraint-invariant penalty to our estimating function. We develop a fast coordinate descent algorithm for estimation, and an augmented Lagrangian algorithm for estimation under null hypotheses. We construct a model-robust score test, and demonstrate valid inference even for small sample sizes and violated distributional assumptions. The flexibility of the approach and comparisons to related methods are illustrated via a meta-analysis of microbial associations with colorectal cancer.

radEmu is here! ❤️🐦📈🔥

The StatDivLab's best differential abundance method yet!

arxiv.org/abs/2402.05231

Nearly 20 years ago, Jill Banfield, Gene Tyson & team transformed #microbiology with their seminal paper on genome-resolved metagenomics. Their innovative approach in reconstructing microbial genomes opened new frontiers in understanding ecosystem dynamics!
paper here: www.nature.com/articles/nat...