Christian Brandt

Bioinformatics, Sequencing, Nextflow, Docker, Cloud, Whisky, Metagenomics, clin. microbiology. CEO of nanozoo

[Christian Brandt @gcloudChris]

Our research with @nanopore 's adaptive sampling has been published (https://t.co/yCIJSgX44S). 'Human host depletion' in clinical metagenomes resulted in increased total sequencing depth, thus higher taxonomic profiling sensitivity while preserving the microbial composition.

[guido werner @guwe33]

Just coming back from a workshop exactly addressing this topic for the situation in 🇩🇪- I am keen to read global experts’ meaning on #AMR genomic surveillance in @TheLancet

[Ryan Wick @rrwick]

New blog post: https://t.co/OWnmLPQs5g

I took the ONT data from my last post, subsampled to various depths and assembled with Flye.

Reveals what ONT-only accuracy looks like with a 'normal' read depth and Flye assembly (as opposed to extra-deep reads and Trycycler assembly).

[Christian Brandt @gcloudChris]

Great Job. A good step by step to set up an easy to use database and to automatically visualize your biological data

[NENG HUANG @csuhuangneng]

New preprint📢 miniBUSCO: a faster and more accurate reimplementation of BUSCO.⚡️Assess assembly completeness for a human genome within 30 minutes⏱️and achieve improved agreement with annotation completeness.🧬Thanks Dr. Li
@lh3lh3 https://t.co/upGNoSG2xc

[Oxford Nanopore @nanopore]

Improvements in latest MinKNOW update:
•5kHz sampling rate replaces 4kHz sampling rate - for improved accuracy
•POD5 is now the default raw data file type
•Addition of 5mC/5hmC Remora Model
•Automatically stop your runs with Run Until

Learn more: https://t.co/1YqCzLtkb0

[Martin Hölzer @martinhoelzer]

Looking forward to the direct RNA update tomorrow #nanoporeconf! Meanwhile, we also updated our preprint on dRNA-seq systematic errors with signal analysis, first is the mismatch error relationship between the 4 bases and their signal features (esp. intensity and dwell time) 1/3

[Lara Urban @LaraUrban42]

After a v successful & exciting day @NanoporeConf @nanopore #NanoporeConf (and an equally successful night in London with science friends @ReindertN @miles_benton @J_MartiCarreras @olga_francino @AaronPomerantz et al), the entire group presents their posters today! Pls come by 🥳

[Oxford Nanopore @nanopore]

Innovation continues towards enabling the analysis of #anythinganyoneanywhere with a new ASIC in development, which is now generating Q20+ sequencing chemistry, and will underpin a new family of lower-cost, lower-power instruments. #nanoporeconf

[Oxford Nanopore @nanopore]

Oxford Nanopore was the first to enable direct RNA sequencing. The new kit (RNA 004) and flow cell for direct RNA sequencing demonstrates increased accuracy and output, with the potential to unlock a new field of biological analysis. #nanoporeconf https://t.co/mchKktqzAd

[Christian Brandt @gcloudChris]

Timeline @nanopore releases

[Mike_Mqt @mult1fractal]

#riseandshine
#NanoporeConf
@gcloudChris
@maralohde
Ready for new knowledge

[Mathias Pletz @DrPletz]

Long-term read sequencing will probably be the future method for ID and AST direct from samples as POCT. https://t.co/wWlEGCqVLL

[Sundar Pichai @sundarpichai]

We're expanding access to Bard in US + UK with more countries ahead, it's an early experiment that lets you collaborate with generative AI. Hope Bard sparks more creativity and curiosity, and will get better with feedback. Sign up: https://t.co/C1ibWrqTDr
https://t.co/N8Dzx1m0fc

[Gregor Kalinkat @[email protected] @gkalinkat]

A short update on the German buzz around #WissZeitVG reform

the reform draft has been cancelled by @sabinedoering (state secretary @BMBF_Bund) for the time being

the weekend has shown why #AcademicTwitter remains essential for organizing and lobbying

#IchBinHanna #IchBinReyhan

[nobody @phiweger]

Finally published our experiments with adaptive @nanopore sequencing to detect antimicrobial resistance genes; TLDR: make sure your database has similar genes and (counterintuitively) longer reads are not always better -- https://t.co/nSPMdLhcZb

[Christian Brandt @gcloudChris]

@RyanCookAMR Is the sequencer actual sequencing less viral dna or is it due to the DNA length per read? E.g. would splitting the reads help or sheering the input DNA?

[Taco Jesse @TJesse62]

PacBio vs Nanopore
@PacBio
@nanopore

- Final version -

Acknowledgements to @khmiga

[Christian Brandt @gcloudChris]

@FalconieriV @SciLifeLab_BMI What program/software are you using to generate these 3d figures. Looks good

[Tom Goldstein @tomgoldsteincs]

#OpenAI is planning to stop #ChatGPT users from making social media bots and cheating on homework by "watermarking" outputs. How well could this really work? Here's just 23 words from a 1.3B parameter watermarked LLM. We detected it with 99.999999999994% confidence. Here's how 🧵

[Jarno N. Alanko @[email protected] & Bluesky @jnalanko]

I asked ChatGPT to write a FASTA parser. It returned a fully working Python implementation with comments and everything. I asked it to port it to Rust. It did that, and produced a correct Rust program that compiles without any warnings. What is this sorcery??!