STing: accurate and ultrafast genomic profiling with exact sequence matches

Abstract

17Genome-enabled approaches to molecular epidemiology have become essential to public health agencies 18 and the microbial research community. We developed the algorithm STing to provide turn-key solutions 19for molecular typing and gene detection directly from next-generation sequence data of microbial 20 pathogens. Our implementation of STing uses an innovative k-mer search strategy that eliminates the 21 computational overhead associated with the time consuming steps of quality control, assembly, and 22