The plot is highly customizable by choosing marks, aggregation, color and size mappings and can be directly exported to publication ready SVG files. We also support exporting the specs back into a datavzrd view for easy reproducibilty and more tweaking.

Our tool #datavzrd has just received a new release adding on the fly scatter plot creation for any two columns of your dataset. @johanneskoester.bsky.social github.com/datavzrd/dat...

We continue to improve bedder. It does interval intersections on VCF, BED, etc and lets users write python expressions on the intersection to drive output (including modifying VCF INFO fields). It will also use an index where possible to avoid extra parsing. Give it a go: github.com/quinlan-lab/...

We just released Polars 2.0. It removed many of our legacy decisions makes the streaming engine our default and promotes SQL to a first class citizen within Polars. pola.rs/posts/releas...

Release of Polars 2.0

DataFrames for the new era

pola.rs

Registration for the #SnakemakeHackathon2027 is open now. This time, it will be at the Paul-Scherrer-Institute in Switzerland. Details and registration: indico.cern.ch/e/snakemake2... Please spread the word!

Snakemake Hackathon March 2027

We are excited to announce the Snakemake Hackathon 2027, to be held 8-12 March, 2027 at the Paul Scherrer Institute, Switzerland. This event will bring together passionate developers and data scientis...

indico.cern.ch

I have just release #rust-bio 4.1.0 containing various bug fixes (e.g. for gap extensions in pairHMMs) and support for IUPAC codes in our homopolymer aware pair HMM flavor (homopolypairHMM).

Our portable alignment viewer #alignoth now supports working with remote BAM files similar to samtools. Simply update to version 1.11 via cargo, conda or pixi and you are good to go. github.com/alignoth/ali... #bioinformatics #genomics #rustlang @johanneskoester.bsky.social

#datavzrd config files now get autocomplete and inline validation right in your editor thanks to schemastore. Just name the file *.datavzrd.yaml and Zed, VS Code and most other IDEs should pick up the schema automatically. @johanneskoester.bsky.social

New in #datavzrd v2.72.0: The suggest command can now draft your report config with any OpenAI compatible LLM endpoint. Describe what you want in plain language and it writes a validated config from your tables. datavzrd.github.io #bioinformatics @johanneskoester.bsky.social

Datavzrd is an awesome tool that turns CSVs into shareable reports that can sort/filter/plot your data, made by @fxwiegand.bsky.social and @johanneskoester.bsky.social You can now run Datavzrd in the browser and rebuild the reports in real time as you edit the config: sandbox.bio/playgrounds/...

Interactive datavzrd playground

Playground for creating interactive reports from tabular data using datavzrd

sandbox.bio

We seek for an experienced bioinformatician to perform #Snakemake based reproducible multi omics data integration in order to decipher melanoma therapy resistance. The project is a DFG funded CRC and might be extended for up to 12 years. Details can be found here: karriere.ume.de/wp-content/u...

Two weeks left to apply! We're recruiting a PhD student with @brianfclarke.bsky.social and @junyanlu.bsky.social through HIDSS4Health - see below for details. 👇 Looking forward to your application.

Brian Clarke@brianfclarke.bsky.social · 3mo ago

Our division is recruiting a PhD student through the Helmholtz Information and Data Science School for Health (HIDSS4Health). The supervision will be joint between me, @oliverstegle.bsky.social and @junyanlu.bsky.social. www.hidss4health.de/application/ → Project ID03 Deadline August 18

New preprint🚨(*long* time coming)! We introduce seqproc: an efficient, flexible, and concise tool for describing and transforming sequencing-read geometry. The aim: make complex protocols easy to specify & transform without giving up speed or accuracy. www.biorxiv.org/content/10.6... 🧵

Pixi v0.75.0 now ships with an --offline mode. Install your environments directly from the shared cache, even on the train or plane! 🛫 Find out more here: pixi.prefix.dev/latest/refe...

We just released a new version of #alignoth that adds support for multiple bam tracks that will get vstacked. Also many convenience features suggested by @johanneskoester.bsky.social such as automatically creating an index for bam, fasta and vcf files if they dont exit. github.com/alignoth/ali...

GitHub - alignoth/alignoth: Creating alignment plots from bam files

Creating alignment plots from bam files. Contribute to alignoth/alignoth development by creating an account on GitHub.

github.com

Another new #datavzrd feature has been released in the form of toggling columns into a narrow view. This allows compressing very wide heatmap-heavy tables into an oncoprint like overview. Thanks for the feature suggestion @johanneskoester.bsky.social datavzrd.github.io

It is now possible to sponsor #snakemake development. Money will go to the Essen University Medicine Foundation and be used for hackathons, computational resources, and personnel: github.com/sponsors/sna...

Sponsor @snakemake on GitHub Sponsors

Support the development of Snakemake. The money will be used for hackathons, computational resources, and depending on the amount, also personnel.

github.com

#rustbio 4.0 has been released. It harmonizes the error handling, improves the API, makes gap-open/extend behavior in pairwise alignment more intuitive and in-line with the literature, improves GFF parsing, and allows incremental building of the rank-select datastructure. github.com/rust-bio/rus...

Release v4.0.0 · rust-bio/rust-bio

4.0.0 (2026-06-12) ⚠ BREAKING CHANGES Replace anyhow with typed thiserror errors (#674) Change Phase conversion methods to use TryFrom for better error handling (#625) for pairwise alignment, only...

github.com

#Snakemake 9.23 has been released. It adds the ability to use gh/gl shorthands for specifying source files (e.g. Snakefiles) from Github oder Gitlab repositories. In addition, source retrieval from Github/Gitlab has been optimized and further secured. snakemake.github.io

A trend to keep an eye on are efforts to develop pocket AIs that can run offline on a single laptop. They're not nearly as powerful as what OpenAI or Anthropic offer, but if free offline options do enough to satisfy normie users the entire business case for so many massive data centres falls apart

After some quite time #datavzrd finally got a new release with an updated binning algorithm ensuring interesting datapoints don’t get swallowed up by one bin. Working on more more features right now!

Another #Snakemake release (9.22.0). We have added a new default pathvar, new semantic helpers for choosing directories or files from alternatives, extended provenance information and Python 3.14 support. In addition various bugs have been fixed. snakemake.github.io

I'm going to try something next month. AI deskilling is real. I'm going a month without it. blog.stephenturner.us/p/ai-dry-july

AI Dry July

AI deskilling is real. I'm going a month without it. 900 words, 4 minutes reading time.

blog.stephenturner.us

It’s amazing how quickly we lose fluency in languages we don’t use frequently. I think many coders are going to find out the hard way that we don’t call programming languages that just for convenience. All to say I like this idea and will likely try the same (outside existing build-AI-to projects.)

Congrats to @leoackermann.bsky.social on winning RECOMB's best poster award for his work on compressing pairwise distance matrices! Check it out here: lacker.gitlab.io/pdf/research...

Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...

Introducing nail - a Rust implementation of profile HMM sequence alignment for proteins. Near-HMMER sensitivity, but a lot faster: www.biorxiv.org/content/10.1... github.com/TravisWheele...

#Snakemake 9.21.1 has been released with lots of bug fixes. In addition, we had several more releases in the past 2 months with improvements for between workflow caching, profile handling, and semantic helper functions. And there is more in the pipeline! snakemake.github.io

Yo; @lh3lh3.bsky.social is in on the AI-assisted RIIR. The future is, literally, now :). Can't wait to try this out!

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 5mo ago

Memory-safe high-performance sequence mapping with rammap https://www.biorxiv.org/content/10.64898/2026.05.26.726289v1

RE: https://fediscience.org/@snakemake/116295568336688286 This is a big step forward: The SLURM plugin for Snakemake now supports so-called job arrays. These are cluster jobs, with ~ equal resource requirements in terms of memory and compute resources. The change in itself was big: The purpose […]