zbecerra/Phylogeographic-analysis-of-S.-nepalensis-carrying-the-intrinsic-sal-E-resistance-gene: Becerra et al. 2026 - Phylogeographic analysis of S. nepalensis carrying the intrinsic sal(E) resistance gene

Bioinformatics pipeline v1.0.0 Complete pipeline used in: Becerra et al. (2026). Phylogeographic analysis of Staphylococcus nepalensis reveals global occurrence of antimicrobial-resistant lineages carrying the intrinsic sal(E) resistance gene. Pipeline includes: Genome download and quality filtering (CheckM2, QUAST) Genome annotation (Bakta v1.12.0) Pangenome analysis (Panaroo v1.3.4) Recombination detection (Gubbins v3.4.2, ClonalFrameML v1.20) Phylogenetic inference (IQ-TREE v3.1.2) AMR profiling (AMRFinderPlus v4.2.7, CARD v3.2.7) Plasmid typing (PlasmidFinder v2.2.0) Structural analysis (AlphaFold3, ChimeraX v1.18.0) Data Genomes: COLB (GenBank: JBDFMR000000000.1) AM1 (GenBank: JBEGDQ000000000.1)