Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!

@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs). If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.

Using ~8M SARS-CoV-2 genomes, a new phylogenetic algorithm by @russcd.bsky.social detects 10 shifts in mutation patterns, some of them linked to changes in viral polymerase. This provides new perspectives on the evolution of mutational processes. 🔗 doi.org/10.1093/molb... #molbio #evobio #covid

POSTDOCS: We're hosting our fourth-annual Next Wave of Faculty in Genomics symposium in beautiful Santa Cruz, CA, to showcase rising talent in genomics research. Travel expenses are covered for selected applicants ✈️😎🏖 APPLY BY JAN 15: genomics.wordpress.ucsc.edu/calendar_eve...