STing: accurate and ultrafast genomic profiling with exact sequence matches. Issue 14 (3rd July 2020)

• Record Type: Journal Article
• Authors: Espitia-Navarro, Hector F; Chande, Aroon T; Nagar, Shashwat D; Smith, Heather; Jordan, I King; Rishishwar, Lavanya
• Is Part Of: Nucleic acids research. Volume 48:Issue 14(2020)
• Page Start: 7681
• Page End: 7689
• Publication Date: 2020-07-03
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa566
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Genome-enabled approaches to molecular epidemiology have become essential to public health agencies and the microbial research community. We developed the algorithm STing to provide turn-key solutions for molecular typing and gene detection directly from next generation sequence data of microbial pathogens. Our implementation of STing uses an innovative k -mer search strategy that eliminates the computational overhead associated with the time-consuming steps of quality control, assembly, and alignment, required by more traditional methods. We compared STing to six of the most widely used programs for genome-based molecular typing and demonstrate its ease of use, accuracy, speed and efficiency. STing shows superior accuracy and performance for standard multilocus sequence typing schemes, along with larger genome-scale typing schemes, and it enables rapid automated detection of antimicrobial resistance and virulence factor genes. STing determines the sequence type of traditional 7-gene MLST with 100% accuracy in less than 10 seconds per isolate. We hope that the adoption of STing will help to democratize microbial genomics and thereby maximize its benefit for public health.