Mastodawn

Martin Hölzer Apr 26, 2023

1st full release of RIBAP!

https://github.com/hoelzer-lab/ribap/releases/tag/1.0.0

RIBAP combines sequence homology info from Roary (kudos to the devs!) w/ clever pairwise ILP calcs (kudos to @klamkiewicz!) to produce a more complete microbial core gene set - even on genus level.

Implemented in @nextflowio

Release Release 1.0.0 · hoelzer-lab/ribap

What's Changed First full-release of RIBAP. Since the last pre-release: We have rewritten our ILP modules to be less harddrive-demanding. per default: ILPs and their solutions are not stored anym...

GitHub

Martin Hölzer Apr 4, 2023

RT @JenaRNA
More jobs at our lab! Are you interested in #phages regulating the gut #microbiome? We have a PostDoc position available: https://www.rna.uni-jena.de/job/postdoc-in-viromics/

Martin Hölzer Mar 31, 2023

Everyone talking about @nanopore DNA sequencing and improving accuracy but you're more into dRNA-Seq? Check out the great work of Liuwei!

- median read accuracy ~90% w/ some species-specific exceptions
- majority Del and homopolymer errors
- C & U more likely to be erroneous
...

Martin Hölzer Mar 31, 2023

Interest in assembling some highly repetitive bacteria genomes? Check it out! Would be now cool to see what the newest @nanopore chemistry can do!
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RT @koebnik_ralf
What you always wanted to know about how best to assemble highly repetitive #Xanthomonas genome sequences and TALomes using short- and long-read sequencing: https://rdcu.be/c8Md5. @BioMedCentral @nanopore @illumina @NEBiolabs @martinhoelzer @mikrobenjaeger @PHIM_researc…
https://twitter.com/koebnik_ralf/status/1641466762162995204

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing | BMC Genomics

Martin Hölzer Mar 25, 2023

RT @GeorgesVis
Four PhD positions available in my group. Deep and unsupervised learning, proteomics, NLP, data visualization, antimicrobial resistance. 🔁 Join us on our mission 🚀 https://interamt.de/koop/app/stelle?0&id=935773
#ArtificialIntelligence #MachineLearning #visualization #Bioinformatics #DataScience #PhD

Stellensuche | Detailinformationen

Doktorandin/Doktorand (mehrere Stellen) - Künstliche Intelligenz & Public Health (m/w/d)

interamt.de

Martin Hölzer Jan 5, 2023

Today, we see n=36 XBB.1.5 sequences in the randomized collection of German SARS-CoV-2 sequences.

Daily updated consensus genomes, lineage assignments, and metadata: https://github.com/robert-koch-institut/SARS-CoV-2-Sequenzdaten_aus_Deutschland)
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RT @rki_de
Auch in Kalenderwoche KW 51 bleibt Omikron in 🇩🇪 dominierende #SARSCoV2-Variante. Gesamtanteil Sublinie BA.5 ist im Vergleich zu Vorwochen weiter leicht gesunken.
#XBB15 wurde erst…
https://twitter.com/rki_de/status/1611014991083192320

GitHub - robert-koch-institut/SARS-CoV-2-Sequenzdaten_aus_Deutschland: Das Robert Koch-Institut stellt Systeme zur bundesweiten molekularen Surveillance des SRARS-CoV-2-Virus bereit. Jedes Labor in Deutschland, das SARS-CoV-2 sequenziert, ist laut der Verordnung zur molekulargenetischen Surveillance des Coronavirus SARS-CoV-2 verpflichtet, dem Robert Koch-Institut die Sequenz- und zugehörige Metadaten zu übermitteln. Technisch erfolgt diese Übermittlung über den Deutschen Elektronischen Sequenzdaten-Hub (DESH).

Das Robert Koch-Institut stellt Systeme zur bundesweiten molekularen Surveillance des SRARS-CoV-2-Virus bereit. Jedes Labor in Deutschland, das SARS-CoV-2 sequenziert, ist laut der Verordnung zur m...

GitHub

Martin Hölzer Dec 23, 2022

When your colleagues give you a 3D-printed coronavirus cookie cutter, you make CoV cookies. Damn, that wasn't easy and I underestimated the time involved! These spikes! 😅

Merry Christmas and may baked viruses be kind to you while all the other viruses out there spare you! 🎄

Martin Hölzer Dec 19, 2022

Wow that sounds amazing! Finally I can just tell R which kind of ggplot I want w/o looking up the syntax :D kudos ad all involved!
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RT @StevenXGe
Happy holidays! Introducing http://RTutor.ai, an AI-powered app that lets you chat with your data in English! RTutor uses Davinci (#ChatGPT’s sibling) to turn requests into R code, which is executed & results are shown instantly, available as a HTML report in seconds. 1/8
https://twitter.com/StevenXGe/status/1604861481526386690

RTutor

Martin Hölzer Dec 14, 2022

Sometime it helps re-assemble raw data from NCBI before going into any comparative analysis. Here a plasmid from a Chlamydia psittaci strain, obtained from NCBI (left) and derived after re-assembly using latest tools. Diffs in homopolymer regions and two larger seq parts missing