Reads2Type: a web application for rapid microbial taxonomy identification

BMC Bioinformatics

Methodology Article

Nizar Haddad¹  Ole Lund²  Thomas Sicheritz-Pontén²  Maria Maddalena Sperotto²  Dhany Saputra²  Simon Rasmussen²  Mette V. Larsen²  Frank M. Aarestrup³ 

[1] Bee Research Department, National Centre for Agricultural Research and Extension, P.O. Box 639, 19381, Baqa’, Jordan;Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, DK-2800, Kgs. Lyngby, Denmark;National Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kemitorvet, DK-2800, Kgs. Lyngby, Denmark;

关键词: Microbial identification;    Marker genes;    Whole genome sequencing;    Bacterial isolate;   

DOI  :  10.1186/s12859-015-0829-0

 received in 2015-04-14, accepted in 2015-11-17,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundIdentification 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.ResultsRaw 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.ConclusionsIn 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.

【 授权许可】

CC BY   
© Saputra et al. 2015