Narciso M Quijada1,2, David Rodríguez-Lázaro2, Jose María Eiros3, Marta Hernández1,2. 1. Laboratory of Molecular Biology and Microbiology, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain. 2. Division of Microbiology, Department of Biotechnology and Food Science, Universidad de Burgos, Burgos, Spain. 3. Servicio de Microbiología y Parasitología, Hospital Universitario del Río Hortega, Valladolid, Spain.
Abstract
MOTIVATION: The progress of High Throughput Sequencing (HTS) technologies and the reduction in the sequencing costs are such that Whole Genome Sequencing (WGS) could replace many traditional laboratory assays and procedures. Exploiting the volume of data produced by HTS platforms requires substantial computing skills and this is the main bottleneck in the implementation of WGS as a routine laboratory technique. The way in which the vast amount of results are presented to researchers and clinicians with no specialist knowledge of genome sequencing is also a significant issue. RESULTS: Here we present TORMES, a user-friendly pipeline for WGS analysis of bacteria from any origin generated by HTS on Illumina platforms. TORMES is designed for non-bioinformatician users, and automates the steps required for WGS analysis directly from the raw sequence data: sequence quality filtering, de novo assembly, draft genome ordering against a reference, genome annotation, multi-locus sequence typing (MLST), searching for antibiotic resistance and virulence genes, and pangenome comparisons. Once the analysis is finished, TORMES generates and interactive web-like report that can be opened in any web browser and shared and revised by researchers in a simple manner. TORMES can be run by using very simple commands and represent a quick an easy way to perform WGS analysis. AVAILABILITY AND IMPLEMENTATION: TORMES is free available at https://github.com/nmquijada/tormes. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: The progress of High Throughput Sequencing (HTS) technologies and the reduction in the sequencing costs are such that Whole Genome Sequencing (WGS) could replace many traditional laboratory assays and procedures. Exploiting the volume of data produced by HTS platforms requires substantial computing skills and this is the main bottleneck in the implementation of WGS as a routine laboratory technique. The way in which the vast amount of results are presented to researchers and clinicians with no specialist knowledge of genome sequencing is also a significant issue. RESULTS: Here we present TORMES, a user-friendly pipeline for WGS analysis of bacteria from any origin generated by HTS on Illumina platforms. TORMES is designed for non-bioinformatician users, and automates the steps required for WGS analysis directly from the raw sequence data: sequence quality filtering, de novo assembly, draft genome ordering against a reference, genome annotation, multi-locus sequence typing (MLST), searching for antibiotic resistance and virulence genes, and pangenome comparisons. Once the analysis is finished, TORMES generates and interactive web-like report that can be opened in any web browser and shared and revised by researchers in a simple manner. TORMES can be run by using very simple commands and represent a quick an easy way to perform WGS analysis. AVAILABILITY AND IMPLEMENTATION: TORMES is free available at https://github.com/nmquijada/tormes. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Nickolas G Kessler; David M Caraballo Delgado; Neel K Shah; Jeff A Dickinson; Sean D Moore Journal: J Bacteriol Date: 2021-03-22 Impact factor: 3.490
Authors: Catalina Díaz-Ríos; Marta Hernández; David Abad; Laura Álvarez-Montes; Athanasia Varsaki; David Iturbe; Jorge Calvo; Alain A Ocampo-Sosa Journal: Antibiotics (Basel) Date: 2021-04-23