BREAKING:
New proposed OMB regulation, applying to all federal grants, requiring grant reviews by senior political appointees and re-emphasizes that "peer review remains advisory and does not replace agency discretion".
#standupforscience
public-inspection.federalregister.gov/2026-10817.pdf
How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well.
In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵
www.biorxiv.org/content/10.6...
public-inspection.federalregister.gov
outside the CDC main entrance today
Identifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174
💉 Did you know, if you live in or are traveling to a measles outbreak area, your baby can receive the measles vaccine as early as 6 months❓
Babies under 12 mo are at highest risk for severe disease from measles. Early vaccination provides critical protection during outbreaks.
public health guy
Please use this page to implement practices in your office to prevent and control measles spread. You’ll find details about measles vaccination recommendations, a sample, customizable measles policy, and tips to help implement it in your office.
www.aap.org
It has been many years since I created Annapotater out of the frustration that there was no simple SNP annotation tool at the time. The mainstream tool required Java and if you wanted to have a custom genome, then it was also a pain.
I gave it a silly name because I thought it was a silly project. A cross between "annotate" and "potato" which was a sort of slang term for bad camera at the time. But I also liked the name because just like a SNP, the name can be pronounced with many different variations.
Early versions were known as the Kapsak Spectac. Congratulations team!!
Annapotater update! I found a very minor thing to change. So there is a new minor version today.
🦑 Kalamari v5.9 adds new outbreak‑relevant viral genomes to the curated set. This includes topical organisms related to ongoing outbreaks: measles, hantavirus, and ebola.
🔗 github.com/lskatz/Kalam...
I finally put it onto Bioconda last night. Give it a go. github.com/lskatz/annap...
