plasmidSPAdes: assembling plasmids from whole genome sequencing data

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: plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ CONTACT:…

• UD
  U.S. Department of Energy
• JG
  Joint Genome Institute
• SP
  Saint Petersburg State University

  Award: 15.61.951.2015