Somak 🥼💻✨️

Does anybody know of any UK-based postdocs that are microbiome / sustainable ag related which are either out or coming up soon and need someone who can run a field site like the military and has an excellent track record in bioinformatics???

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 ...

💾 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...

This is why @wytamma.bsky.social and I have been writing SNIPPY-NG ! It will support short reads, long reads, and assemblies as inputs. You can check it out at github.com/centre-patho...

It's not ready for prime-time yet, but it's useable!

GitHub - tseemann/snippy: :scissors: Rapid haploid variant calling and core genome alignment :scissors: :zap: Rapid haploid variant calling and core genome alignment - GitHub - tseemann/snippy: :scissors: Rapid haploid variant calling and core genome alignment

Slightly out of context but snippy too is a great variant calling tool.. @torstenseemann.bsky.social could add support for long reads? 😄

github.com/tseemann/sni...

This should help with the -x flag…

github.com/barricklab/b...

Murder-suicide case shows OpenAI selectively hides data after users die OpenAI accused of hiding full ChatGPT logs in murder-suicide case.

LLMs.

They promote suicide and murder, undermine a century of educational practice, drive deskilling, harm the environment, and benefit foreign adversaries spreading disinformation.

But the federal government wants to prohibit states from regulating them.

You'd think they were guns.

gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota Microbiota-derived metabolites serve as key messengers mediating host–microbe and microbe–microbe interactions, often through specialized primary meta…

Now available online: the new 2.0 version of gutSMASH, with capabilities to detect 12 new types of catabolic gene clusters relevant to gut microbiome ecology, as well as predictions of their regulation through transcription factor binding site detection. www.sciencedirect.com/science/arti...

Amazing tool. Any plans to release a singularity or docker container of this. Will be of massive help..

Evaluating long-term stool preservation methods for maximizing the recovery of viable human fecal microbiota The gut microbiome plays a fundamental role in human health, prompting efforts to catalog and preserve its diversity across human populations. While DNA sequencing dominates microbiome research, cu...

Found this resource www.tandfonline.com/doi/full/10....

Sorry meant 0.1%. A lot of tinkering at db level might be needed before the illumina v4-v5 could be analysed.

Would it make sense to create otu bins till 99% at 1% increments and gather a representative sequence? The repset could be made into a strain blast db or bowtie index. No. Of mapped reads to strain db divided by total reads should give strain level relative abundance from v4 regions.

Full length 16S data is from Sanger seq or extracted from wgs denovo assembly?

Rookie scientists make research teams more innovative Papers from research teams with a substantial number of beginners are highly disruptive and innovative, study shows.

Papers from research teams with a substantial number of beginners are highly disruptive and innovative

go.nature.com/4nrEvqg

Gene co-occurrence and its association with phage infectivity in bacterial pangenomes | Philosophical Transactions of the Royal Society B: Biological Sciences Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or can...

Gene co-occurrence and its association with phage infectivity in bacterial pangenomes

Phil. Trans. R. Soc. B by @annecmg.bsky.social et al
with @fbaumdicker.bsky.social

royalsocietypublishing.org/doi/10.1098/...

Welcome to #bluesky team CEH shoutout to Tim from India this time!

Vacancy — Assistant Professor in Microbiome Imaging and Functional Analysis Are you pioneering molecular tools and applying advanced imaging strategies to uncover how microbial communities are organized and interact in space and time? If so, we invite you to join The Swammerd...

Assistant Professor position in the Microbiome Engineering group (Prof Sahar El Aidy) at University of Amsterdam

Assistant Professor in Microbiome Imaging and Functional Analysis
werkenbij.uva.nl/en/vacancies...

Great to see our Review "The gut microbiome connects nutrition and human health" making the cover of this month's @natrevgastrohep.nature.com

@patrickveiga.bsky.social @eranelinav.bsky.social
www.nature.com/articles/s41...

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

Hi #microbiome folks, Do you have a custom recipe that is used for anaerobic faecal sample preservation during collection and transport at room temp? Need it for samples whose fate is culturomics.
#gutmicrobiome

Hi #microbiome folks, Do you have a custom recipe that is used for anaerobic faecal sample preservation during collection and transport at room temp? Need it for samples whose fate is culturomics.
#gutmicrobiome

Keeping it behind a landing page with necessary forms and authentication is also reasonable as long as wait times are not too long imho.

There is no problem in wanting to know how many times and by whom data has been accessed. But if no personal identity info is part of the data then i see no reason why in the age of figshare, sra and other open repos intent to share is hiding behind this tactic.

Data not shared = science didnt happen.

Journals should do a test request and then send notice why such papers shouldn’t be retracted.

🧬🖥️ Postdoc positions available SOON!!
Looking for researchers with strong computational skills (programming essential) to work on microbiome & phylogenetics projects.
📅 Start on Nov 1, 2025 (flexible)
📍 Trento, Italy
DM me for details or share!
#postdocjobs #microbiome #metagenomics #phylogenetics

Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria - Microbiome Background Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, the...

Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria

-in BMC Microbiome

microbiomejournal.biomedcentral.com/articles/10....

If bclconvert is done then output of that too passed to multiqc for a detailed summary

Fastqc with fastp summarized using multiqc when sample numbers are very large.

Guidelines for preventing and reporting contamination in low-biomass microbiome studies - Nature Microbiology In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize contaminants.

I think this is a paper every microbiome scientist should read:
www.nature.com/articles/s41...

New vacancy in my team!

PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.

Please repost and share with talented MSc students in #evobio, bioinformatics or related :)

www.uu.nl/en/organisat...

#MEvoSky #MicroSky

antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation Abstract. Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in

We're happy to announce that the #antiSMASH v8 paper is out in @narjournal.bsky.social: academic.oup.com/nar/advance-...
Many thanks to @kblin.bsky.social, @marnixmedema.bsky.social and many international collaborators!