plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data

Abstract

ABSTRACT Motivation Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell’s chromosomes. Although plasmids harbor biomedically important genes, (such as genes involved in virulence and antibiotics resistance), there is a shortage of specialized software tools for extracting and assembling plasmid data from whole genome sequencing projects. Results We present the plasmidSPAdes algorithm and software tool for assembling plasmids from whole genome sequencing data and benchmark its performance on a diverse set of bacterial genomes. Availability and implementation PLASMID SPA DES is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ Contact [e-mail]