plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data

Abstract

MotivationPlasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cells 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.\n\nResultsWe 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.\n\nAvailability and implementationO_SCPCAPPLASMIDC_SCPCAPSPAO_SCPCAPDESC_SCPCAP is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/\n\nContactd.antipov@spbu.ru