plasmidSPAdes: assembling plasmids from whole genome sequencing data

Dmitry Antipov; Nolan Hartwick; Max Shen; Mikhail Raiko; Alla Lapidus; Pavel A Pevzner

doi:10.1093/bioinformatics/btw493

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.

Authors

Dmitry Antipov¹, Nolan Hartwick², Max Shen³, Mikhail Raiko², Alla Lapidus¹, Pavel A Pevzner^{1

2}

Affiliations

¹ Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
² Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
³ Bioinformatics and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA.

PMID: 27466620
DOI: 10.1093/bioinformatics/btw493

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.

MeSH terms

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