High-performance tools for precise microbiome characterization

Abstract

The microbiome, defined as the vast number of microorganisms inhabiting both human and non-human environments, has been associated with human disease as well as other important ecological phenomena. However, its quantitative study is complicated in part by measurement error and computational limitations, pointing to a need for more sensitive and reproducible DNA sequence analysis techniques. To this end, I have developed a variety of improved methods including a flexible short-read quality control pipeline, curated databases of marker genes and whole genomes, streamlined OTU picking software, and a high-throughput optimal aligner with taxonomy interpolation. Together, these methods represent advancements over traditional sequence analysis pipelines and may improve the quality of downstream statistical analyses.