Taxonomic Profiling & Strain-Level Typing — Hands-on

Build reproducible taxonomic profiling workflows for shotgun metagenomes and push to strain-level resolution when needed. You'll compare k-mer and marker-gene profilers, choose and manage reference databases (GTDB, UHGG, RefSeq/GenBank) , quantify abundance with bias awareness, and perform strain tracking with tools like StrainPhlAn, inStrain, MIDAS, and PanPhlAn. Includes QA/QC with mock communities and benchmarking against CAMI-like datasets.