plasmidSPAdes: assembling plasmids from whole genome sequencing data

Bioinformatics. 2016 Nov 15;32(22):3380-3387. doi: 10.1093/bioinformatics/btw493. Epub 2016 Jul 27.


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 CONTACT: d.antipov@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Algorithms
  • Genome, Bacterial*
  • Plasmids / genetics*
  • Sequence Analysis, DNA
  • Software