Self-hosted ResFinder AMR annotation with anomaly-scored resistance calls (k-mer + PubMed-enriched)

A self-hosted ResFinder-based annotation pipeline, combined with 21-mer k-mer AMR screening and a multi-signal anomaly scoring layer, can flag likely resistance-conferring sequence anomalies with fewer false positives than raw ResFinder hits alone without requiring cloud submission of genomic data.

My Reasoning: Standard ResFinder calls resistance genes by homology but doesn’t contextualize hits against expected codon usage or population-level co-occurrence patterns, which produces false positives in noisy assemblies. Our pipeline layers three orthogonal signals on top of raw calls: GC-content Z-score deviation, Codon Adaptation Index (Sharp & Li 1987) relative to host organism, and a co-occurrence matrix built from [50K clinical isolates / BV-BRC confirm exact N and source before posting]. The premise is that a resistance-gene call flagged as anomalous on multiple axes simultaneously is more likely to reflect a real, expressed resistance element than a single-signal ResFinder hit.