Mohammad Jamhuri

Measuring and removing near-duplicate contamination in alignment-free SARS-CoV-2 lineage classification benchmarks

Alignment-free lineage assignment from k-mer frequency profiles is widely used for SARS-CoV-2 surveillance, and the methods that do it are ranked against each other by margins of one or two percentage points. Those rankings rest on an unchecked protocol. Public repositories hold many near-duplicate genomes, and stratif...