Reads2Resistome: An adaptable and high-throughput whole-genome sequencing pipeline for bacterial resistome characterization

Abstract

SummaryThe bacterial resistome is the collection of all the antibiotic resistance genes, virulence genes, and other resistance elements within a bacterial isolate genome including plasmids and bacteriophage regions. Accurately characterizing the resistome is crucial for prevention and mitigation of emerging antibiotic resistance threats to animal and human health. Reads2Resistome is a tool which allows researchers to assemble and annotate bacterial genomes using long or short read sequencing technologies or both in a hybrid approach. Using a massively parallel analysis pipeline, Reads2Resistome performs assembly, annotation and resistome characterization with the goal of producing an accurate and comprehensive description of a bacterial genome and resistome contents. Key features of the Reads2Resistome pipeline include quality control of input sequencing reads, genome assembly, genome annotation, resistome characterization and alignment. All prerequisite dependencies come packaged together in a single suit which can easily be downloaded and run on Linux and Mac operating systems. AvailabilityReads2Resistome is freely available as an open-source package under the MIT license, and can be downloaded via GitHub (https://github.com/BioRRW/Reads2Resistome).