New blog post! I reran the Autocycler paper benchmarks on some new tools/versions/pipelines: rrwick.github.io/2026/07/24/b... (1/3)

Very proud of this preprint out of my lab, our first (of hopefully many) host-microbe spatial transcriptomics paper. www.biorxiv.org/content/10.6... Amazing insights into P. aeruginosa biology and chronic airway disease @cysticfibrosis.org.uk @sangerinstitute.bsky.social @asthmaandlung.org.uk

Read: 'Phylo-Plex: A phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology' in @natcomms.nature.com here 👇 https://www.nature.com/articles/s41467-026-75002-y

Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology

Nature Communications - Whole genome sequencing of pathogens is costly to implement, and partial sequencing sacrifices information. Here, the authors present Phylo-Plex, a method for identifying...

nature.com

Like Artemis/ACT but wish it was easier to install and more modern? Try Seqhiker. 🧬 Native desktop app (no Java) for Windows/mac/linux 🖱️ Drag-n-drop FASTA/GenBank/GFF3/BAM/VCF files 🔍 Genome browsing and ACT-style comparison ✨ Themes (customisable) and a Vim mode Docs: seqhiker.readthedocs.io

Deacon can now run in the browser using WebAssembly. Sequence data never leaves your machine. It currently supports FASTA/Q filtering using indexes up to 1GB in size. Demo: bede.im/deacon

Can't wait to release a 10-year-old birthday version for SeqKit! - 10 years - 2 papers, 3500 citations - 20 contributors - 40 subcommands - 880 commits - 500 issues - 685.5K Bioconda total downloads Thank you all, dear contributors and users! I'll keep maintaining it. github.com/shenwei356/s...

Release SeqKit v2.13.0 (10-year-old birthday version) · shenwei356/seqkit

Changelog SeqKit is 10 years old! SeqKit v2.13.0 - 2026-02-28 seqkit: add support for reading and writing LZ4 compression format. new command: seqkit sample2: improved seqkit sample by @stahiga....

github.com

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods

This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

nature.com

What a day for Prog albums! Big Big Train, and the 13 year wait for new Karnivool is over. Both 🔥

Ziplign published in JOSS. Tool to easily interactively compare two bacteria genomes. Inspired by ACT, but easier to install and use. Drag and drop files, or download using accessions. It runs blast for you. No terminal needed. github.com/martinghunt/...

Journal of Open Source Software@joss-openjournals.bsky.social · 8mo ago

Just published in JOSS: 'Ziplign: a simple-to-use interactive tool to compare bacterial genomes' https://doi.org/10.21105/joss.09004

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...

Three roles currently advertised, all to help us develop and validate genetic pipelines for processing pathogens with EIT Oxford. RA/PDRA (Grade 6/7) noon 10 Feb bit.ly/4jANpAc Senior Bioinformatician (G8) 12 Feb bit.ly/4hcMB3b Senior Medical Statistican (G8) 14 Feb bit.ly/4hcMEfn

I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e

We're thrilled to introduce LexicMap v0.5.0🎉 It's more accurate and slightly faster! LexicMap has helped some scientists align genes and plasmids in AllTheBacteria and GenBank, each has > 2 million prokaryotic genomes! We'll provide an index for ATB on AWS later. github.com/shenwei356/L...

📣 New TNA release 0.2.0. What's changed? Search for sequence or annotation. Download genomes from NCBI. Copy/paste sequence. Better performance - can now handle large numbers of BLAST hits instead of freezing. tna.readthedocs.io/en/v0.2.0/in... github.com/martinghunt/...

Release Version 0.2.0 · martinghunt/tna

Added: Option to download genomes instead of providing files Search for nucleotide sequence Search for annotation features Copy selected sequence to clipboard. Line length configurable in Settings...

github.com

Good news, Altmetric has now started watching BlueSky for mentions of publications. And by the way, provides an easy comparison between this and the old site for a recent preprint of mine which I posted simultaneousl at both. Numbers speak by themselves !

🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀 Check it out here: doi.org/10.1101/2024... And find the code here: github.com/mbhall88/lrge 🧵👇

I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io