plasmidSPAdes: assembling plasmids from whole genome sequencing data

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 sof...

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Published inBioinformatics (Oxford, England) Vol. 32; no. 22; pp. 3380 - 3387
Main Authors Antipov, Dmitry, Hartwick, Nolan, Shen, Max, Raiko, Mikhail, Lapidus, Alla, Pevzner, Pavel A.
Format Journal Article
LanguageEnglish
Published England 15.11.2016
Subjects
Algorithms
Genome, Bacterial
Plasmids - genetics
Sequence Analysis, DNA
Software
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Summary: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.
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ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btw493