plasmidSPAdes: assembling plasmids from whole genome sequencing data.
Bioinformatics 2016;
32:3380-3387. [PMID:
27466620 DOI:
10.1093/bioinformatics/btw493]
[Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/11/2016] [Accepted: 07/16/2016] [Indexed: 12/24/2022] Open
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.
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