iiinova — where your digital self keeps evolving

Martin Hunt @martibartfast.bsky.social · 09/09/2026

Mykrobe2 released! mykrobe2.readthedocs.io It's a Go rewrite (AI-assisted) of mykrobe. Has same usage and essentially identical output, but more than twice as fast (mykrobe2.readthedocs.io/en/latest/my...). GUI desktop app is back for Windows, Mac, and Linux. Command line simpler to install

mykrobe2.readthedocs.io

Mykrobe2

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Reposted by Martin Hunt

Ryan Wick @rrwick.bsky.social · 24/07/2026

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

rrwick.github.io

Benchmark update: Ilesta, Autocycler-fast and new versions

a blog for miscellaneous bioinformatics stuff

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Reposted by Martin Hunt

Josie Bryant @josiebryant.bsky.social · 08/07/2026

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

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Martin Hunt @martibartfast.bsky.social · 26/06/2026

Seqhiker also replaces Ziplign. It can run the genome comparison for you and supports >2 genomes in ACT-mode.

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Martin Hunt @martibartfast.bsky.social · 26/06/2026

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

seqhiker.readthedocs.io

The Seqhiker's Guide

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Reposted by Martin Hunt

Bede Constantinides @bede.im · 03/03/2026

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

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Reposted by Martin Hunt

Wei Shen 沈伟 @shenwei356.bsky.social · 27/02/2026

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...

github.com

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....

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Reposted by Martin Hunt

Zamin Iqbal @zaminiqbal.bsky.social · 26/02/2026

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...

allthebacteria.readthedocs.io

Overview — AllTheBacteria documentation

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Reposted by Martin Hunt

Zamin Iqbal @zaminiqbal.bsky.social · 09/02/2026

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)

nature.com

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.

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Martin Hunt @martibartfast.bsky.social · 06/02/2026

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

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Martin Hunt @martibartfast.bsky.social · 02/02/2026

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/...

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Reposted by Martin Hunt

Zamin Iqbal @zaminiqbal.bsky.social · 19/05/2025

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...

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Martin Hunt @martibartfast.bsky.social · 29/04/2025

Is a great paper! I have vague memories of an option that meant you don’t get all the matches (not that you get zero matches), but irrelevant seeing as you’re getting the first hit

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Modernising Medical Microbiology @modmedmicro.bsky.social · 31/01/2025

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

bit.ly

Job Details

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Reposted by Martin Hunt

Andrew Page @andrewjpage.bsky.social · 10/01/2025

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

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Reposted by Martin Hunt

Wei Shen 沈伟 @shenwei356.bsky.social · 19/12/2024

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...

One-page introduction of LexicMap, a sequence alignment tool scalable to millions of prokaryotic genomes.

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Martin Hunt @martibartfast.bsky.social · 16/12/2024

@julianparkhill.bsky.social I've added annotation (and sequence) search. It's in a the new release 0.2.0

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Martin Hunt @martibartfast.bsky.social · 16/12/2024

📣 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/...

github.com

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...

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Reposted by Martin Hunt

Carlos M Herrera @cmhmaliani.bsky.social · 02/12/2024

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 !

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Reposted by Martin Hunt

Michael Hall @mbhall88.bsky.social · 03/12/2024

🌟 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 🧵👇

doi.org

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Martin Hunt @martibartfast.bsky.social · 29/11/2024

Thanks! Good idea, I’ll add that to the list of features to implement

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Martin Hunt @martibartfast.bsky.social · 29/11/2024

You guessed it! Yes, that’s the acronym

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Martin Hunt @martibartfast.bsky.social · 29/11/2024

TNA is like a “minimal ACT”, but with extra features I’ve always wanted: easy Mac install, handle multi-FASTA files, run BLAST for you, show detailed alignment when zoomed in (SNPs/indels), easy contig revcomp/reordering, save/load to/from one file

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Martin Hunt @martibartfast.bsky.social · 29/11/2024

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

tna.readthedocs.io

TNA documentation — TNA 0.0.1 documentation

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