title: SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.
abstract: CONCLUSIONS
  Spoligotyping is a well-established genotyping technique based on the presence of unique DNA sequences in Mycobacterium tuberculosis (Mtb), the causal agent of tuberculosis disease (TB). Although advances in sequencing technologies are leading to whole-genome bacterial characterization, tens of thousands of isolates have been spoligotyped, giving a global view of Mtb strain diversity. To bridge the gap, we have developed SpolPred, a software to predict the spoligotype from raw sequence reads. Our approach is compared with experimentally and de novo assembly determined strain types in a set of 44 Mtb isolates. In silico and experimental results are identical for almost all isolates (39/44). However, SpolPred detected five experimentally false spoligotypes and was more accurate and faster than the assembling strategy. Application of SpolPred to an additional seven isolates with no laboratory data led to types that clustered with identical experimental types in a phylogenetic analysis using single-nucleotide polymorphisms. Our results demonstrate the usefulness of the tool and its role in revealing experimental limitations.
  
  
  METHODS
  SpolPred is written in C and is available from www.pathogenseq.org/spolpred.
  
  
  BACKGROUND
  francesc.coll@lshtm.ac.uk.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics Online.
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. francesc.coll@lshtm.ac.uk
authors.forename: Francesc
authors.initials: F
authors.lastname: Coll
authors.forename: Kim
authors.initials: K
authors.lastname: Mallard
authors.forename: Mark D
authors.initials: MD
authors.lastname: Preston
authors.forename: Stephen
authors.initials: S
authors.lastname: Bentley
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Ruth
authors.initials: R
authors.lastname: McNerney
authors.forename: Nigel
authors.initials: N
authors.lastname: Martin
authors.forename: Taane G
authors.initials: TG
authors.lastname: Clark
mesh_terms: D015373:Bacterial Typing Techniques; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D012984:Software; D014376:Tuberculosis / Q000382:microbiology*