TORMES: an automated pipeline for whole bacterial genome analysis

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.