A BLAST from the past: revisiting blastp's E-value biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

I'm happy to share the results of my rotation with Heng Li: biorxiv.org/content/10.110… We co-assembled reads from paired tumor-normal samples, then examined the structure of the co-assembly graph to identify large-scale somatic structural variation (focusing on translocations)

I finally got around to testing HERRO (github.com/lbcb-sci/herro), the new Oxford Nanopore read correction algorithm which takes simplex ONT reads to PacBio-HiFi-level accuracy. I was impressed! Findings are on my blog in a two-part post: rrwick.github.io/2024/07/26/her… rrwick.github.io/2024/07/31/her…

One of my mentees just completed his second project with me: SciKit-Jax: github.com/LiibanMo/sciki… Scikit-Learn does not leverage GPUs by itself and offers less flexibility in the model design. Scikit-Jax solves these! He will polish this to accommodate multi-GPU setups once we

my boomer bioinfo take is that if reads are *unaligned* then they should not be stored in a SAM/BAM file.

SynGAP: a synteny-based toolkit for gene structure annotation polishing genomebiology.biomedcentral.com/articles/10.11…

A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread. academic.oup.com/nar/advance-ar…

Spaln3 by Osamu Gotoh: academic.oup.com/bioinformatics…

One of the reasons I've been quiet on Twitter for a few months is because I've been working on something big - something I'm really happy to share now! Pathoplexus.org A new, open-source database for pathogen sequence sharing. 👐🧬🌎 1/12

A new type of microbe discovered in the human gut! Called obelisks, they can create their own proteins that are entirely new to science. The team named their proteins “oblins.” Scientists scratching their heads about it biorxiv.org/content/10.110…

Preprint on "BWT construction and search at the terabase scale". We can compress 100 human genomes to 11GB in 21 hours, find SMEMs with it, do affine-gap alignment and retrieve similar local haplotypes. 7.3Tb commonly sequenced bacterial genomes ⇒ 30GB arxiv.org/abs/2409.00613

Come join our team! We are hiring a bioinformatics pipeline engineer, a backend software engineer, and a full-stack software engineer.

Amazing and comprehensive guide to adding, updating and debugging bioinformatics software tools on Bioconda by James Fellows Yates | @[email protected] (expanding on his earlier blogpost) - if you do bioinformatics software dev, it is truly all you need to get started with Bioconda

I'm starting my own scientific journal with @Curvenote Journals! ScienceUX.org will have 🔬research ⬇️#opensource tools 👨‍🏫teaching materials ...for making science easier for scientists to do via better design. Video intro ▶️ buff.ly/4dkZ3ex

1/11 Excited to share our latest paper in @GenomeResearch: "Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements" 🧬🦠 The Banfield Lab

The backstory behind the FASTA bioinformatics format youtu.be/7LA0IKsVloU?si… via YouTube

New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30

Refs this paper nature.com/articles/s4146… which describes new mycoplasma-related symbionts of coral with strange, reduced genomes #Microbiology #Evolution #Genomics #Symbioses

Did you know that BLAST searches used to be done by email?! I went down quite the rabbit hole for this video: youtu.be/imXQDiIsyjA

I don't post much here, but recently the #content I see here is rarely relevant to me I finally explored bluesky and was excited to see basically everyone there! If you're waiting, the community has moved to bluesky and that's where you'll find me -- (@)matt-mcguffie