🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2

New tgv release: local cache!

tgv download hg38

Download UCSC reference genomes to a local sqlite db for much faster browsing. Awesome Rust tools (twobit, bigtools) made this simple.

github.com/zeqianli/tgv

New figure for my thesis showing why Giraffe is the best long read pangenome mapper. No further evidence will be provided.

A couple of months ago I tried the @peercommunityin.bsky.social publishing system & I can only recommend it (pun intended). Please see below to change how we publish science 1/n

Researchers at @ucsantacruz.bsky.social have demonstrated how long-read sequencing could improve detection of diseases that have eluded diagnosis, at a fraction of the cost. New clinical tests could be on the way.
🗞 news.ucsc.edu/2025/01/pate...
👏🏼👏🏿👏🏾 @khmiga.bsky.social @benedictpaten.bsky.social

Organising the EMGM in Brest next year: emgm2025.sciencesconf.org

Hurray for cats (and regulatory mutations)

"We engineered approximately 45,000 insertions, 6,000 deletions and 41,000 amino acid substitutions across the nearly 2,200 coding positions of the Enterovirus A71 proteome, quantifying their effects on viral fitness"
www.nature.com/articles/s41...

40 years later, and we still don't have a good answer. (original article is quite fun: www.jstor.org/stable/24084...)

1/ 🧵 Free resources for scientists

💡 Covering research skills, careers, #SciComm, leadership, activism and more, everything in this thread appears on our Learning Resources page, with tips for researchers and academics at any career stage. #AcademicChatter #ECRChat
https://buff.ly/4f8vIpk

🎨 In case anyone need…

The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!

Check it out 👇
bioart.niaid.nih.gov

The barley pangenome paper is finally out. 🎉
#genomics
rdcu.be/d0ecz

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience

We have a method for fast GWAS data access. STABIX adds a p-value index that with a position index (what TABIX has) allows you to quickly retrieve, eg. all significant SNPs in a target gene. Also column compression to reduce the size. www.biorxiv.org/content/10.1...

github.com/kristen-schn...

📣 Preprint alert! We have studied the formation of pair-wise and multi-way enhancer-promoter interactions in the #3Dgenome in a lymphoid-to-myeloid transdifferentiation system and learned interesting new things about their function in #GeneRegulation. 1/10
www.biorxiv.org/content/10.1...