Tessera
Folgen

Pratik Katte

@pratikkatte.bsky.social

PhD in computational bio @UCSC • Understanding evolution• building ARGs at scale • http://lorax.ucsc.edu • https://pratikkatte.github.io/

2 Posts14 Follower19 Folgt
Pratik Katte@pratikkatte.bsky.social · 2mo ago

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

Lorax

lorax.ucsc.edu

Jeffrey Ross-Ibarra@jrossibarra.bsky.social · 5mo ago

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!

GitHub - RILAB/argprep: Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files.

Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files. - RILAB/argprep

github.com

Molecular Biology and Evolution@molbioevol.bsky.social · last yr.

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

A Phylogenetic Method Identifies Candidate Drivers of the Evolution of the SARS-CoV-2 Mutation Spectrum

Abstract. The molecular processes that generate new mutations evolve, but the causal mechanisms are largely unknown. In particular, the relative rates of m

doi.org