1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN).
👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...
#EVD68 #Enterovirus #OpenData
My sense is to maybe check out canu. I don't know how well any polisher would be with a ploidy > 1 though.
Would think flye with long-read and polish using short-read with pypolca. Granted I don't know how complex your genome is, but I've had good success with 8 chr fungi (albeit haploid).
New in @plosone.org : Amplicon sequencing of pasteurized retail dairy reveals H5N1 avian influenza virus in U.S. cattle milk. Tiled-amplicon NGS achieved >90% genome coverage from pasteurized milk samples, enabling genomic surveillance of H5N1 spillover in cattle. journals.plos.org/plosone/arti...
It’s Black Inclusion Week this week. If you are a Black microbiologist we would recommend connecting with the Black Microbiologists Association. They are working hard to increase visibility and facilitate connections: blackinmicrobiology.org #BlackInMicro #BIW2025
T7 is short enough that they can be designed at the 5' end of an oligo
I think it's a good idea, otherwise you are liking driving overexpression of downstream genes, or their antisense RNA (which may prevent translation). Or could mess up plasmid stability if it's replication is based on RNA like ColE1
T7 terminator or rrnB T1T2 I used to use frequently
Are these optimized promoter sequences for strong constitutive expression? Perhaps you don't need as much product made, and can use a less efficient sequence?
Conversely clone into a lower copy number plasmid?
Transcriptional terminators may help.
A new version of our Mtb pangenome preprint is out! Expanded analysis of the full pangenome data and answering all those questions the reviewers asked for ;). Great working with
@mabi-behruznia.bsky.social @danwhiley.bsky.social @blackpassiflora.bsky.social and others
www.biorxiv.org/content/10.1...
Mathew effect
“…early funding success introduces a growing rift, with winners just above the funding threshold accumulating more than twice as much research funding (€180,000) during the following eight years as nonwinners just below it.”
www.pnas.org/doi/10.1073/...
Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons. Published #OpenAccess and fee-free in #MGen using a #PublishAndRead agreement: https://doi.org/10.1099/mgen.0.001312
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...
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One of the reasons I've been quiet on Bluesky for a few months is because I've been working on something big - something I'm really happy to share now! Pathoplexus.org
A new, open-source database for pathogen sequence sharing. 👐🧬🌎
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This is v impressive from @pathogenomenick.bsky.social and Co. Trap mosquitoes with CO2 (dry ice), and by sequencing them+bloodmeal+viruses, you get information on host, vector and arboviruses. Piloted in Sao Paolo.
www.microbiologyresearch.org/content/jour...
1. Canadian researchers publish the first estimates of 2023-24 #flu vaccine effectiveness that I've seen to date, in Eurosurveillance. The VE is pretty good — 61% overall against H1N1, which was responsible for the vast majority of cases.
#EpiSky www.eurosurveillance.org/content/10.2...
My attempt
