Tandem: a bioinformatics tool for detection, mechanism classification, and population quantification of bacterial tandem gene duplications (opens in new tab)

Motivation: Tandem gene duplication drives antibiotic resistance, metabolic adaptation, and gene-family expansion in bacteria, but no tool detects them in reference genomes, discovers their junctions in isolate sequencing, and quantifies the junctions in population samples. Existing callers (e.g. breseq) detect duplications without classifying formation mechanisms and often fail to quantify the duplication. Results: Tandem has 3 modules. Module 1 detects reference-genome duplications by NUCme...