Pangenomes, but scalable.
Panmap: phylogeny-guided framework for read alignment, genotyping, sample placement on pangenomes. 600x smaller indexes, faster builds, and placement from 20K to 8M genomes. @amkram.bsky.social @alanbyzhang.bsky.social @russcd.bsky.social
www.biorxiv.org/content/10.6...
Pangenomes, but scalable.
Panmap: phylogeny-guided framework for read alignment, genotyping, sample placement on pangenomes. 600x smaller indexes, faster builds, and placement from 20K to 8M genomes. @amkram.bsky.social @alanbyzhang.bsky.social @russcd.bsky.social
www.biorxiv.org/content/10.6...
Excited to be presenting my poster on Lorax at #PEQG26!
Lorax is a GPU-accelerated, web-native tool for real-time interactive visualization of Ancestral Recombination Graphs.
If you're at Asilomar this week, come check it out. Would love to chat about scalable ARG exploration and get your feedback
www.biorxiv.org
www.biorxiv.org
Alex Kramer, Alan Zhang and friends posted our preprint today. In it, we introduce Panmap, a tool for phylogenetic placement, assembly, lineage abundance estimation, and eDNA assignment using phylogenetic pangenomes.
www.biorxiv.org/content/10.6...
Pratik Katte
Pratik Katte
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...
@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
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!
Russ Corbett-Detig
Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files. - RILAB/argprep
Abstract. The molecular processes that generate new mutations evolve, but the causal mechanisms are largely unknown. In particular, the relative rates of m
