title: Reads2Type: a web application for rapid microbial taxonomy identification.
abstract: BACKGROUND
  Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institutions and routine diagnostic microbiology laboratories may need to sequence the entire genome of microbial isolates. Therefore we have developed Reads2Type, a web-based tool for taxonomy identification based on whole bacterial genome sequence data.
  
  
  RESULTS
  Raw sequencing data provided by the user are mapped against a set of marker probes that are derived from currently available bacteria complete genomes. Using a dataset of 1003 whole genome sequenced bacteria from various sequencing platforms, Reads2Type was able to identify the species with 99.5 % accuracy and on the minutes time scale.
  
  
  CONCLUSIONS
  In comparison with other tools, Reads2Type offers the advantage of not needing to transfer sequencing files, as the entire computational analysis is done on the computer of whom utilizes the web application. This also prevents data privacy issues to arise. The Reads2Type tool is available at http://www.cbs.dtu.dk/~dhany/reads2type.html.
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark. dhany@cbs.dtu.dk.
authors.forename: Dhany
authors.initials: D
authors.lastname: Saputra
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark. simon@cbs.dtu.dk.
authors.forename: Simon
authors.initials: S
authors.lastname: Rasmussen
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark. metteb@cbs.dtu.dk.
authors.forename: Mette V
authors.initials: MV
authors.lastname: Larsen
authors.affiliation: Bee Research Department, National Centre for Agricultural Research and Extension, P.O. Box 639, Baqa', 19381, Jordan. drnizarh@yahoo.com.
authors.forename: Nizar
authors.initials: N
authors.lastname: Haddad
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark. maria@cbs.dtu.dk.
authors.forename: Maria Maddalena
authors.initials: MM
authors.lastname: Sperotto
authors.affiliation: National Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark. fmaa@food.dtu.dk.
authors.forename: Frank M
authors.initials: FM
authors.lastname: Aarestrup
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark. lund@cbs.dtu.dk.
authors.forename: Ole
authors.initials: O
authors.lastname: Lund
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark. thomas@cbs.dtu.dk.
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Pontén
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D019985:Benchmarking; D002965:Classification; D004269:DNA, Bacterial / Q000235:genetics; D030541:Databases, Genetic; D016680:Genome, Bacterial; D020407:Internet; D058885:Multilocus Sequence Typing; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012984:Software
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S