title: SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads.
abstract: SpoTyping is a fast and accurate program for in silico spoligotyping of Mycobacterium tuberculosis isolates from next-generation sequencing reads. This novel method achieves high accuracy for reads of both uniform and varying lengths, and is about 20 to 40 times faster than SpolPred. SpoTyping also integrates the function of producing a report summarizing associated epidemiological data from a global database of all isolates having the same spoligotype. SpoTyping is freely available at: https://github.com/xiaeryu/SpoTyping-v2.0 .
authors.affiliation: NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore. xiaeryu@u.nus.edu.
authors.forename: Eryu
authors.initials: E
authors.lastname: Xia
authors.affiliation: NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore. statyy@nus.edu.sg.|Centre for Infectious Disease Epidemiology and Research, Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore. statyy@nus.edu.sg.|Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore. statyy@nus.edu.sg.|Life Sciences Institute, National University of Singapore, Singapore, Singapore. statyy@nus.edu.sg.|Genome Institute of Singapore, Singapore, Singapore. statyy@nus.edu.sg.
authors.forename: Yik-Ying
authors.initials: YY
authors.lastname: Teo
authors.affiliation: Centre for Infectious Disease Epidemiology and Research, Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore. twee_hee_ong@nuhs.edu.sg.
authors.forename: Rick Twee-Hee
authors.initials: RT
authors.lastname: Ong
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D003198:Computer Simulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D012984:Software; D013997:Time Factors; D014376:Tuberculosis / Q000382:microbiology*