Are reads required? High-precision variant calling from bacterial genome assemblies

This repository holds methods, code and data for our manuscript:
Wick RR, Judd LM, Stinear TP, Monk IR. Are reads required? High-precision variant calling from bacterial genome assemblies. bioRxiv. 2025. doi:10.1101/2025.02.20.639404.

Contents:

• data/: tarballs of all assemblies and VCFs created in the study
• figures/: all main-text and supplementary figures
• scripts/: all custom scripts used in the analysis
• methods.md: all commands run for the analysis
• tables.xlsx: Supplementary tables