If using conda, consider miniforge as the installer. It does not utilize defaults channel unless explicitly requested by the user (e.g. -c) github.com/conda-forge/mi…

🚨 New Courses Alert! 🚨 Explore our latest APHL Learning Platform self-paced courses on Viral Amplicon Genomic Characterization & Genomic Epidemiology! 📚🌍 Designed for a global public health audience, these trainings include lecture videos, slides, exercises & mock datasets.

It's almost my favorite time of year again. Teaching students how to read phylogenies using Pokemon.

🎉Bactopia v3.1.0 is here!🕺 This release brings fun changes to the Bactopia Nextflow pipeline! Two named workflows, clean-yer-reads and teton, are now available, as well as new Bactopia Tools! Get started at: bactopia.github.io/v3.1.0/ #bioinformatics #genomics

LoVis4u v0.0.9 is released. Now with new compact styles for A4 layouts, including one- and two-column figures with adjusted fonts and object sizes. Check out the examples in the gallery and visit the new user guide page: art-egorov.github.io/lovis4u/Galler…

A regular reminder, the GitHub Stars are more than a pretend point system. They can be used as a metric when applying for grants (e.g. continued support)! If like a tool, support it by "starring" it's Github repo! haha maybe even Bactopia's repo github.com/bactopia/bacto… 😍

Last week joined our colleagues & great speakers in the #MENAMicrobiome conference Sidra Medicine. We had a great panel discussion about fostering Microbiome collab. in the MENA region.Also presented our Hospital Microbiome Cartography work in the Center for Microbial Medicine at CHOP & CHOP Research

We’re proud to announce that we’re establishing the African Bioinformatics Institute to advance genomics on the African continent. We’re funding the institute together with @chanzuckerberg over the next five years. Learn more ⤵️ wellcome.org/news/were-esta…

Thankful for the opportunity to speak at #ASMNGS about the work we're doing at the WPHL 🦬 to further improve Bactopia! (haha also🏔️!) Per the usual, reach out if you have any questions! Slides are available at: bactopia.github.io/latest/impact-… #nextflow #bioinformatics #bacteria

I've made a new framework for developing sequence based typing (SBT) tools. 🐪camlhmp ("camel hump") allows for an SBT schema to be defined in YAML, disentangling the SBT logic from the code, making much easier to maintain. See poster or learn more at: rpetit3.github.io/camlhmp/latest/

We already have many fantastic registrations for the Snakemake hackathon 2025 at CERN! But there are still some free seats left. Make sure to apply/register soon if you want to shape the future of Snakemake! indico.cern.ch/event/snakemak…

New version of LoVis4u is released! 💛 Now it supports visualisation of non-coding features like tRNAs and includes a new module for hmmscan searches against DefenseFinder, PADLOC, VFDB, AMRFinder, dbAPIS (anti-defences), or your own databases. Homepage: art-egorov.github.io/lovis4u

Hundreds of thousands of genomes, and Nextflow barely breaks a sweat! Recently used Bactopia to process ~650k assemblies from Zamin Iqbal #AllTheBacteria (ATB) project! ATB: allthebacteria.readthedocs.io Using Bactopia with ATB: bactopia.github.io/latest/blog/20… #NextflowSummit #FOMO🥲

Ah, I just tagged new releases for seqkit (github.com/shenwei356/seq…), taxonkit (github.com/shenwei356/tax…), csvtk (github.com/shenwei356/csv…), and rush. There are a lot of changes, please have a look.

Excited to share BakRep - our latest work published in Microbiology Society #MGen >661,000 bacterial genomes, uniformly characterized & annotated, enriched with metadata, accessible via a flexible search engine doi.org/10.1099/mgen.0… 👇 1/7

🦠🧬💻 Bakta v1.10 - largest update so far: Highlights: - user-provided HMMs: --hmms - output file recovery from JSON files: bakta_io - export of inference metrics: inference.tsv - bypass overlap filters: --skip-filter - improved genome plots github.com/oschwengers/ba… 👇 (1/11)

The past six days have been devastating for APHL and the broader global health community. APHL was forced to make the extremely difficult decision to halt all global public health work supported by the U.S. government, directly affecting over 100 employees. Our work has been

🦠🧬🖥️ New Bakta DB v6.0 released! After a year, it was time for a Bakta database update - and it's a huge one: - IPS: 330.9M - PSC: 135.3M - PSCC: 37M doi.org/10.5281/zenodo… 👇 1/6

Thrilled to finally debut my lab site 🎉: mbio.info — which stands for Microbial Bioinformatics, a domain I purchased 9 years ago and has been waiting for this moment ever since!"