Oskar Karlsson

PhD in pathobiology, researching microbial communities and their host interaction. Opinions are mostly my own althoug I'm known to retweet smart stuff...

[Oliver Schwengers 🇩🇪🇪🇺🇺🇦 @oschwengers1]

Having a tool that is used by others is great, one that's evaluated by others is even better, and one that's positively evaluated and endorsed by others - just makes your day as a main developer 😃 More on Bakta at our poster P-MDE-10, tomorrow #VAAM2024 #DGHMVAAM2024

[SciLifeLab_DataCentre @SciLifeLab_DC]

Congratulations to the launch of the @scilifelab Training Portal!!🎇
https://t.co/Ogr6fCqojV

#training #courses #datadriven #lifescience #OpenScience #develop #tools #pedagogy #FAIR

[Chenxin Li, PhD (@chenxinli2.bsky.social) @ChenxinLi2]

A new tutorial on how to reorder rows & columns of a heatmap has been added to my "Friends don't let friends make bad graphs" repository.

Link to tutorial: https://t.co/pRrzngXsii

Link to "Friends don't let friends make bad graphs": https://t.co/KeSsEcs3DS

[Robert A. Petit III, PhD @rpetit3]

🔥 Bactopia v3 is here! 🔥

The @nextflowio pipeline for bacterial genomes is now faster, packed with more tools, updated docs, and much much more!

Get started at: https://t.co/NgRTKuKqeJ

#bioinformatics #genomics

[Ann Lindberg @ann_lindberg]

Som ett första steg i bekämpandet av afrikansk svinpest har Jordbruksverket fastställt en smittad zon. Området sträcker sig från Norberg i norr till Ramnäs i söder, Västerfärnebo i öst och Vad i väst. https://t.co/XRtGYJQd8T

[Ann Lindberg @ann_lindberg]

Tyvärr Sveriges första fall av afrikansk svinpest på vildsvin konstaterats utanför Fagersta. Samverkan mellan ett stort antal aktörer pågår. Målsättning att lokalisera, avgränsa och bekämpa. https://t.co/Y4z10bYYNd

[John Lees @johnlees6]

Pangenome annotations, pangenome annotations, get your pangenome annotations. Accurate and fast, right here
https://t.co/BQo3HN1FDx
@SamuelHorsfield @gerrythill
(ggcaller now out in Genome Research)

[John Lees @johnlees6]

We're making final additions to ska2 (https://t.co/HtwgcxI5MB) -- thanks for everyone that's been using it and given feedback!
@themaklin has written a tutorial on how to use it to rapidly build a tree for some bacterial genomes: https://t.co/Fzkbkjly6l

[Michael Schatz @mike_schatz]

Super excited to announce our new VGP-ERGA-Galaxy pipeline for scalable, accessible, and reproducible reference genome assembly. In just a few clicks anyone anywhere can assemble their genome to VGP quality! @genomeark @galaxy @erga_biodiv https://t.co/BIM3pL9ZqU

[Andreas Sjödin @druvus]

Happy to see the article "Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial" online. Thanks to all reviewers! Adding synbiotic to infant formula seems to give favourable effects of the gut microbiota.
https://t.co/DgdTTy9EbF

[MultiQC @MultiQC]

New release! @MultiQC version 1.14 just hit the shelves, and it's a big one! 🎉 Massive thank you to everyone who contributed (there were a lot of you!) 🙇🏻‍♂️

https://t.co/U4C9HrYH9V

Here's a short thread covering some of the highlights.. 🧵

[Christian Landgren 🦋 @Landgren]

På samma sätt som Twitter klarar sig ”bra” utan 75% av sin personal så funderade jag på vad som skulle hända om Stockholms stad drog bort allt underhåll och personal från Skolplattformen. Läs nedan en tråd om vad som faktiskt pågår varje månad i Skolplattformen🧵

[Anne-Lie Blomström @AL_Blomstrom]

High-throughput sequencing reveals the diversity of viruses in Pipistrellus pygmaeus bats 🦇 from Sweden through great collaboration with @haricholleti et al. https://t.co/COFujlaNzH @VirusesMDPI @SLU_Virology @_SLU

[The Nobel Prize @NobelPrize]

BREAKING NEWS:
The 2022 #NobelPrize in Physiology or Medicine has been awarded to Svante Pääbo “for his discoveries concerning the genomes of extinct hominins and human evolution.”

[Oskar Karlsson @Metaviromics]

@AMB_SLU @MariaWesterholm @annaschnurer Ohhhh, fancy beard Simon rocks these days!

[Maja Malmberg @majamalmberg @malmberg_maja]

New great paper by @Hedvig_Stenberg et al., out now in @SpringerNature! "Congenital tremor and splay leg in piglets – insights into the virome, local cytokine response, and histology". Thank you @StinaHellman @juliette_hayer @_SLU @KSLA_Academy https://t.co/P0Zd5Y6vyo

[Heng Li @lh3lh3]

Miniprot, a new mapper for aligning proteins to genomes with splicing and frameshift. Can be used for annotating new genomes. ~20k mouse proteins to the human genome in 5 mins over 16 threads. Still WIP. Feedback welcomed. https://t.co/ILAvmF3VBO

[Anne Carpenter, PhD @DrAnneCarpenter]

2 years ago, everything was going great in my mid-career lab.

Making a choice to reduce stress and prioritize my health turned out to have ripple effects - my colleagues, family, and friends are reaping the benefits, as am I.

I tell my story in @eLife
https://t.co/UmSmRCBtht

[Torsten Seemann @torstenseemann]

Bakta is a worthy successor to Prokka, which has been neglected in recent years. Bakta is being actively developed with new features that Prokka never had, so I encourage Prokka users to try it out!

[Oskar Karlsson @Metaviromics]

@KlingstromT Grattis!