TY - JOUR

T1 - Reads2Type

T2 - a web application for rapid microbial taxonomy identification

AU - Saputra, Dhany

AU - Rasmussen, Simon

AU - Larsen, Mette V

AU - Haddad, Nizar

AU - Sperotto, Maria Maddalena

AU - Aarestrup, Frank M

AU - Lund, Ole

AU - Sicheritz-Pontén, Thomas

PY - 2015/11/25

Y1 - 2015/11/25

N2 - 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 https://www.cbs.dtu.dk/~dhany/reads2type.html.

AB - 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 https://www.cbs.dtu.dk/~dhany/reads2type.html.

KW - Bacteria/classification

KW - Bacterial Proteins/genetics

KW - Benchmarking

KW - Classification

KW - DNA, Bacterial/genetics

KW - Databases, Genetic

KW - Genome, Bacterial

KW - Internet

KW - Multilocus Sequence Typing

KW - RNA, Ribosomal, 16S/genetics

KW - Software

U2 - 10.1186/s12859-015-0829-0

DO - 10.1186/s12859-015-0829-0

M3 - Journal article

C2 - 26608174

VL - 16

JO - B M C Bioinformatics

JF - B M C Bioinformatics

SN - 1471-2105

M1 - 398

ER -