I will present a number of techniques (namely: Quikr, EMDeBruijn, and CommonKmers) that I’ve recently developed in collaboration with colleagues, and discuss the advantages and disadvantages of applying these techniques in a variety of circumstances. Quikr is an extremely fast, high level taxonomic profiling tool suitable for understanding the global structure of many metagenomics samples. EMDeBruijn is a reference free, de Bruijn graph-based approach to quantifying the similarities and differences between metagenomic samples, even in the presence of many novel microbial organisms. Finally, CommonKmers is a new, highly accurate taxonomic profiling technique capable of faithfully profiling a community down to the strain level. This technique can then use the resulting taxonomic profile to inform the assembly of a metagenome.