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Bioinformatics. 2016 Nov 15;32(22):3380-3387. Epub 2016 Jul 27.

plasmidSPAdes: assembling plasmids from whole genome sequencing data.

Author information

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.

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.

PMID:
27466620
DOI:
10.1093/bioinformatics/btw493
[Indexed for MEDLINE]

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