Integrated AMR profiling (AMRFinderPlus) + 23S rRNA linezolid-resistance frequency analysis
linezolid-amr combines NCBI AMRFinderPlus gene/mutation detection on an assembly with species-aware mapping of raw reads to 23S rRNA references to detect heteroresistant linezolid-resistance mutations (e.g. G2576T, G2505A) in Staphylococcus aureus, Enterococcus faecalis/faecium, Streptococcus pneumoniae, and Mycobacterium tuberculosis. The same --organism flag drives both AMRFinderPlus species mode and 23S reference selection. Mutations are reported in E. coli K-12 23S numbering (the clinical-literature convention) via a pairwise-alignment-derived position map computed at fetch time.
