Quantitive bioinformatic studies are a mainstay of modern microbiome research. Despite almost 15 years since the first studies were published, a wide variety of techniques exist for analysis with new techniques emerging every year. In this review, we explore the latest developments in sample preservation, extraction, and sequencing. We describe new bioinformatic developments in both marker-gene and metagenomic sequencing. While these represent novel analytical approaches, in 2020 and beyond, we look forward to better benchmarks of the existing tools.