"Sure, bedtools is great and happily used by literally everyone, but, it could be bedder" That takes some serious courage. Kudos Brent and @aaronquinlan.bsky.social !

1/2 #NearLab @chasedbrownstein.bsky.social described Birmingham Darter Etheostoma birminghamesnse in April 2025 It is under threat from a mega data center. A petition was filed yesterday by the @biologicaldiversity.org to review the species for protection under the ESA www.wbrc.com/2025/11/14/n...

New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/

Another hit from @alabamarivers.bsky.social and Southern Exposure

🌿Plant pangenomes🌿 have a LOT of genomic presence-absence-variation. Or do they??? A new @jgi.doe.gov preprint by @tomasbruna.bsky.social @jotlovell.bsky.social @avril-m-harder.bsky.social Avinash Sreedasyam takes a closer look www.biorxiv.org/content/10.1...

'Hoods are out!!! Big thank you to @plantevolution.bsky.social for the support throughout. Luisa, @kdm9.bsky.social , @aconga.bsky.social , @hajkdrost.bsky.social it was intellectually stimulating ride with you, so congratulations!!!! #diversity #NLR #immune #pan-genome #graphs #networktheory

my new idea is to look at runs of homozygosity (ROH) only for mutations that are restricted to heterozygous state in other pops, suggesting they are low freq. and enriched for deleterious stuff. a good measure of inbreeding. I call my new statistic

This began as a @jgi.doe.gov Community Science Program (CSP) project in 2017 with the goal of uniting the diverse sorghum breeding and mapping populations in the framework of a 'pangenome'. Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:

🚨 We're looking for a #postdoc to join our team at the Center for Bioenergy Innovation at Oak Ridge National Labs, TN 🚨 Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics Apply by 18-Aug Apply here: jobs.ornl.gov/job/Oak-Ridg...

Ok, fine I'm willing to admit it now: Mimulus is interesting www.authorea.com/doi/full/10....

That time in 2013 when this crabeater seal decided to see what this noisy orange menace was doing in its territory....In 2013 near Peter I Island in #Antarctica on our research cruise (LMG 13-12). Bonus (the 'wait for it' at the end): amazing sunset/sunrise around 1am that night :) 🧪🌎🦑🐧🇦🇶

Wow, the cover looks great! Nice work Patrice and @roederlab.bsky.social The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome

Clever new BUSCO-like method to evaluate the quality of pangenome graphs www.biorxiv.org/content/10.1...

Quick break from the doom and gloom for science! We're really proud of this one. We found that two major effect loci on duplicated versions of the same ancestral chromosome play a major role in run timing diversity across four species of salmon (pink, chum, sockeye, coho) shorturl.at/GISX2

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...

Post a warning.

"Our results reveal substantial differences between pipelines, with many inversions either misrepresented or lost. Most notably, recovery rates remain strikingly low, even with the most simple simulated genome sets, highlighting major challenges in analyzing inversions in pangenomic approaches."

Our paper on the past, present, and genomics-enabled future of American chestnut (Castanea dentata) tree breeding for resistance to invasive pathogens is on BioRxiv. 🧵with some background and a few things we found 👇 bsky.app/profile/bior...

A new version of our variation graphs (vg) tool, "Boccaleone," is now available! Updates include: 🔵 HiFi and Oxford Nanopore read support to the Giraffe read mapper 🔵 Faster read sorting 🔵 New Unix manual page Link: github.com/vgteam/vg/re...

Welcome to Day 2 of #PAG32 | #PAG2025. Today's cant miss session is Comparative Genomics hosted by Vijay Tiwari and John Lovell. It is 10:30 - 12:40 in Pacific A. pag.confex.com/pag/32/meeti...

Are you headed to #PAG32 and interested in plant reproduction? 🌼 Come check out my talk in the “Sex Chromosomes and Sex Determination” session on Saturday! I’ll be talking about ancient ZW sex chromosomes, the impact of polyploidy on sexual system evolution, “leaky” dioecy, and much more.

What's better than one polyploid genome? Twelve polyploid genomes! We report a pangenome of the hexaploid oilseed crop Camelina sativa and investigate pangenomic variation and genome evolution in a complex allopolyploid genome. www.biorxiv.org/content/10.1...

Our groups' goal is to produce genomes that are useful; this does not always mean 'telomere-to-telomere' assemblies. The hybrid sugarcane genome is a nice example of this. The article is out this week in Nature: www.nature.com/articles/s41...

@ksamuk.bsky.social pointed this out on the other site, but I don't see much discussion here. GATK will now encode missing genotypes as "0/0", or homozygous ref, instead of "./." in VCF files. To identify sites with missing data, you'll have to check the DP field.

🚨We're hiring🚨 We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO. Pls share! hudsonalpha.applicantpro.com/jobs/3211389

A new study shows that flowers have evolved over the past three decades to have less sex—potentially in response to the disappearance of bees. It could be a death spiral for some species. Here’s my story. 🧪 Gift link: www.nytimes.com/2024/01/04/s...