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plasmidSPAdes: assembling plasmids from whole genome sequencing data

Author:
Antipov, Dmitry, Hartwick, Nolan, Shen, Max, Raiko, Mikhail, Lapidus, Alla, Pevzner, Pavel A.
Source:
Bioinformatics 2016 v.32 no.22 pp. 3380-3387
ISSN:
1460-2059
Subject:
algorithms, bioinformatics, chromosomes, computer software, genes, plasmids, sequence analysis, virulence
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.ru Supplementary information: Supplementary data are available at Bioinformatics online.
Agid:
6247576