Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Nov 15;32(22):3380-3387.
doi: 10.1093/bioinformatics/btw493. Epub 2016 Jul 27.

plasmidSPAdes: assembling plasmids from whole genome sequencing data

Dmitry Antipov  1 , Nolan Hartwick  2 , Max Shen  3 , Mikhail Raiko  2 , Alla Lapidus  1 , Pavel A Pevzner  1   2
Affiliations

plasmidSPAdes: assembling plasmids from whole genome sequencing data

Dmitry Antipov et al. Bioinformatics. .

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: plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ CONTACT: d.antipov@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer