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...
It sure is fun!
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)
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/...
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...
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
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
One-page introduction of LexicMap, a sequence alignment tool scalable to millions of prokaryotic genomes.
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...
@julianparkhill.bsky.social I've added annotation (and sequence) search. It's in a the new release 0.2.0
📣 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/...
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
🧵👇
Thanks! Good idea, I’ll add that to the list of features to implement
You guessed it! Yes, that’s the acronym
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
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
