Biochemistry, Biophysics, and Structural Biology Commons^™

Census-Based Rapid And Accurate Metagenome Taxonomic Profiling, Amirhossein Shamsaddini, Yang Pan, W. Evan Johnson, Konstantinos Krampis, Mariya Shcheglovitova, Vahan Simonyan, Amy Zanne, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

Background

Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis.

Results

Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive …