Wytamma

GitHub - PathoGenOmics-Lab/VIPERA: A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis - PathoGenOmics-Lab/VIPERA

VIPERA v1.2.2 is out!! 🐍

now you can swap in different stats (useful for non-linear allele freq trends). also: new Docker images on release, containerized CI, updated envs, and minor bug fixes for smoother, reproducible intra-patient SARS-CoV-2 analyses

🧪👉 github.com/PathoGenOmics-Lab/VIPERA

The geospatial phylodynamics of SARS-CoV-2 in Nepal and clinical phenotype of long COVID during the Delta-Omicron waves The COVID-19 pandemic exposed gaps in global emerging infectious disease preparedness, particularly for countries with high levels of economic migration, such as Nepal. The Epidemic Intelligence proje...

Our study on SARS-CoV-2 dynamics and long COVID in Nepal has made it to preprint 🎉 Huge thanks everyone from BNMT, Center for Molecular Dynamics Nepal (CMDN), and the Centre for Pathogen Genomics at The Peter Doherty Institute for Infection and Immunity 👏👏👏

www.medrxiv.org/content/10.1...

Had a great time at #SMBE2025 presenting our work of bacterial genome classification with AI github.com/bloodhound-d...

A call to save the date for MicroSeq2025, returning September 3-4. MicroSeq is an online meeting where microbiology meets sequencing, including bacteria, viruses, and fungi.

🦋Hello BlueSky!🦋 Let's get right into it. MicroSeq is back September 3-4, 2025! Stay tuned for more details on registration and abstract submission coming soon here and at www.microseqconference.com. 🌟Save the date!🌟
#MicroSeq2025

The BEAST X logo - an octopus wrapping its noodley appendages round the letter X.

BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...

Details and instructions for installing on the BEAST website: beast.community

News - Community urged not to touch bats after rare case of Australian bat lyssavirus NSW Health confirms first bat lyssavirus case in 2025. Avoid handling bats and seek urgent care if bitten or scratched. Only trained experts should manage injured bats.

Only the fourth case of ABLV in humans. Although ABLV is classified as a different species to rabies virus, the disease is more of less rabies: www.health.nsw.gov.au/news/Pages/2...

🎉

Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...

Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!

Screenshot of the homepage of Pathoplexus, showing tiles to navigate to the supported pathogens CCHF, Ebola Sudan, Ebola Zaire, HMPV, Mpox, RSV-A, RSV-B, and West Nile virus.

📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.

These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.

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Please move genomes to an open pathogen platform like pathoplexus.org!

It’s starting to look like you might need some long reads to resolve your assembly graph 😂

Core Bioinformatics team at QIB -- job offer to join the team as bioinformatics programmer as per link

Hello binfies 👋!

There is an open position for a senior bioinformatician to join our fab **core bioinformatics** team at @quadraminstitute.bsky.social.

jobs.quadram.ac.uk/Details.asp?...

Prompt injection is a feature not a bug

Snippy: Microbial Variant Calling Community Survey Help us drive the next wave of innovation in Single-Nucleotide Polymorphism (SNP) discovery and genome analysis by sharing your valuable experiences and insights. This in-depth survey aims at understa...

🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...

How much did this bad boy cost to make? Like low 10s of millions?

Dorado v0.9.1 now includes a bacterial model for genome polishing, so I put it to the test! How does it compare to Medaka? And does move-table data improve polishing accuracy? Read my analysis here:
rrwick.github.io/2025/02/07/d...

Are you referring to LLMs or generative AI in general?

GitHub - Wytamma/open-sci-scroller Contribute to Wytamma/open-sci-scroller development by creating an account on GitHub.

SciScroller is an open source Svelte app that is statically hosted on GitHub pages -> github.com/Wytamma/open...

Semantic Scholar | AI-Powered Research Tool Semantic Scholar uses groundbreaking AI and engineering to understand the semantics of scientific literature to help Scholars discover relevant research.

SciScroller uses the free www.semanticscholar.org API (❤️) to search for papers related to a particular research topic.

SciScroller - Scroll Open Science Explore and manage research papers in an innovative scrollable format. SciScroller makes academic discovery faster and easier.

Introducing SciScroller 🔬 - it’s like TikTok for open scientific papers -> sciscroller.wytamma.com

I guess it’s more teleological than utility but agree the technology is over hyped

Visualizing All ISBNs — $10k by 2025-01-31 This picture represents the largest fully open “list of books” ever assembled in the history of humanity.

In the closing hours of the Anna’s Archive $10,000 dollar challenge there are a bunch of submissions rolling in. My favourite is Hypha A‘s Gilbert curve 🔥 -> archive.anarchy.cool/maps/isbn.html

In Australia we call them yeah nah people 😂 I guess what's your utility function? Like is it categorical, in general generating things is not useful? Or is it a quality thing like it's not useful because in general generative AI produces poor quality results?

I’d be keen to hear from the Yes, No people. Overhyped sure, but not useful?

GitHub - Wytamma/cat Contribute to Wytamma/cat development by creating an account on GitHub.

It's a client-side web app written in Svelte that uses streams to process files without loading them all into memory. Your files never leave your computer so it's safe to use on sensitive data. Open source code here - github.com/Wytamma/cat

I often have to concatenate a bunch of text files together so I made this `dag and drop` app to streamline the process 📄📄📄➡️📄 - cat.wytamma.com

Exploring SNP filtering strategies: the influence of strict vs soft core Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental ...

Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets.
www.microbiologyresearch.org/content/jour...
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What’s your Saturday playlist?

Yes I love biowasm! I submitted a PR to biowasm/Aioli that halves the memory usage when in streaming mode (it was keeping a second copy of the output) here's a demo streaming minimap2 output to indexedDB.

blog.wytamma.com/wasm-test-in...
github.com/Wytamma/wasm...