R

RSSC_sequevar_typing

Project information

A Snakemake pipeline for Ralstonia solanacearum species complex (RSSC) sequevar typing based on the endoglucanase (egl) gene. The pipeline extracts the egl gene from bacterial genome assemblies via in-silico PCR, trims it to the ~698 nt phylogenetically informative region, aligns query sequences with curated reference sequevars, builds a maximum-likelihood phylogenetic tree, and produces an annotated tree visualization. Finally, it assigns a sequevar to each query genome based on the nearest reference in the tree. This workflow enables rapid and reproducible sequevar typing for RSSC genomes.

21 Commits
1 Branch
1 Tag
1 Release

README
MIT License
CHANGELOG

Created on

March 13, 2026

Loading