PGTB

Do you want to annotate your #pangenome graph and its embedded genome ? Then GrAnnoT is for you !
🖥️🧬 🧪

In the present paper, our PhD student Nina Marthe developed a Python tool, a user friendly one, that allows to
1/5

www.biorxiv.org/content/10.1...

Comment est-ce que ça pourrait mal se passer ?...

Aux Etats-Unis, Trump et Musk déciment à coups de licenciements la NOAA, vigie de la météo et du climat En une semaine, l’Agence d’observation océanique et atmosphérique a perdu 10 % de ses 12 000 employés, licenciés sur fond de croisade antiscience du gouvernement américain. Une manifestation mondiale de chercheurs est prévue le 7 mars.

🇺🇸 Aux Etats-Unis, Trump et Musk déciment à coups de licenciements la NOAA, vigie de la météo et du climat

En une semaine, l’Agence d’observation océanique et atmosphérique a perdu 10 % de ses 12 000 employés, licenciés sur fond de croisade antiscience du gouvernement américain.

Lire 👇

Are reads required? High-precision variant calling from bacterial genome assemblies Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...

New preprint is out!
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.

Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)

Roche SBX sequencing by expansion preprint out for everyone to read. #NGS #NextGenSequencing

#SBX Fast WGS Clinical Benchmarking: Successfully detects small variants (SNV, Indel), large CNVs (duplications, deletions), and STR expansions in clinical samples, including Fragile X (856 CGG repeats in FMR1), Duchenne MD, and DiGeorge Syndrome. #AGBT25 #AGBT2025 #AGBT @AGBT @Roche

YouTube video by Roche Introducing Roche Sequencing by Expansion (SBX) Technology

New Roche sequencing process to come. Promising!
youtu.be/G8ECt04qPos?...

m.genome.cshlp.org/content/earl... Matt Loose in Nottingham publishes a method for Adaptive Sampling with Oxford @nanoporetech.com sequencing.

Doge staffers enter Noaa headquarters and incite reports of cuts and threats Members reportedly sought access to IT systems at agency that Project 2025 has called ‘harmful to US prosperity’

Incroyable.

Les sbires de Trump et Musk sont entrés de force au sein de l'agence météorologique nationale (NOAA), pour lui couper les vivres et bloquer l'information climatique.

Une atteinte gravissime aux sciences, à la démocratie, à l'avenir.

www.theguardian.com/us-news/2025...

Testing a new DNA extraction protocol on a bee sample @lipme-toulouse.bsky.social.
@nanoporetech.com assembly is impressive. Looks like most of the 16 chromosomes are single T2T contigs!
Thanks @tiboleroyinen.bsky.social and your team for providing the larvae sample!

Baisse annoncée du budget de la recherche et de l’enseignement supérieur : quel avenir pour la recherche scientifique ? Le projet de loi de finances 2025, adopté hier au Sénat, prévoit un coup de rabot conséquent sur le budget de la recherche et de l’enseignement supérieur, avec 630 millions d’euros d’économies. Ces re...

"➕de 50% des chercheurs et enseignants chercheurs vont partir à la retraite d'ici 2030.
Si la France ne réinvestit pas pour rendre ces métiers attractifs, elle décrochera à l'international".
Dean Lewis.
👉 @franceinter.fr : www.radiofrance.fr/franceinter/...

Je viens de faire mon #eXit! L’exode de X est massif. Ne perdez pas un seul de vos abonnés. Grâce à #OpenPortability j’ai inscrit 1682 nouveaux passagers pour partir vers #BlueSky & #Mastodon. Retrouvez automatiquement vos communautés le #20Janvier via app.openportability.com !

GitHub - aakechin/NGS-PrimerPlex: NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design - aakechin/NGS-PrimerPlex

github.com/aakechin/NGS...

🌟 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

🧵👇

Despite being listed as an author, I had no involvement in "writing" this book. It appears to include content taken from freely available CC BY publications, including ours. To save $69, you can access our study for free in @newphyt.bsky.social:
doi.org/10.1111/nph....
#OpenAccess #Anthocyanins

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)

Elon Musk takes aim at Wikipedia The billionaire has become one of the most prominent supporters of President-elect Donald Trump.

If you've never donated to Wikipedia, now's the time. Elon Musk is attacking it because it's one of the only sources of honest, curated information that he can't control.
www.newsweek.com/elon-musk-ta...

x.com/AW_NGS/statu...

genomes.atcc.org/genomes

x.com/theBentoLab/...

x.com/razoralign/s...

x.com/gnomesnerd/s...

www.genomeweb.com/sequencing/w...

ggdist: Make a Raincloud Plot to Visualize Distribution in ggplot2 The ggdist package is a ggplot2 extension that is made for visualizing distributions and uncertainty. We'll show see how ggdist can be used to make a raincloud plot.

www.business-science.io/r/2021/07/22...

Image shows a spider and a paper preview on bioRxiv

If you’re doing DNA barcoding in a fieldwork or resource-limited context and you want to improve phylogenetic resolution at lower cost, here’s a method that allows the sequencing of 3 unlinked regions using long amplicon PCR and @nanoporetech.com MinION for ~€5 a sample.

📷 Timothy Dykes

devider: long-read reconstruction of many diverse haplotypes Reconstructing haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling se-quencing erro...

We built a new tool for disentangling local haplotypes from long-read sequencing: check out devider! github.com/bluenote-157...

www.biorxiv.org/content/10.1...

1/5

Infamous paper that popularized unproven COVID-19 treatment finally retracted Study on hydroxychloroquine by Didier Raoult and colleagues gets pulled on ethical and scientific grounds

It took four days from submission to publication, and nearly five years from publication to retraction. After campaigning by many, many scientists, and an investigation by Elsevier, an infamous paper on hydroxychloroquine as a COVID-19 treatment has been retracted. 🧪
www.science.org/content/arti...

Just had my first experience with CycloneSEQ data and shared my findings in this blog post:
rrwick.github.io/2024/12/17/c...

How does CycloneSEQ compare to @nanoporetech.com? I looked at both read-level and consensus-level accuracy. Check it out!

For anyone interested in PCR enhancers, here’s a new study looking at nine readily accessible compounds that can be used with difficult DNA templates, examining their effects on polymerase thermostability, inhibitors, and amplification of various DNA targets.