title: plasmidSPAdes: assembling plasmids from whole genome sequencing data.
abstract: 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.
  
  
  
  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.
  
  
  
  plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ CONTACT: d.antipov@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Antipov
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
authors.forename: Nolan
authors.initials: N
authors.lastname: Hartwick
authors.affiliation: Bioinformatics and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA.
authors.forename: Max
authors.initials: M
authors.lastname: Shen
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Raiko
authors.affiliation: Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.affiliation: Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.|Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000465:Algorithms; D016680:Genome, Bacterial; D010957:Plasmids / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software