plasmidSPAdes: assembling plasmids from whole genome sequencing data
2016; Oxford University Press; Volume: 32; Issue: 22 Linguagem: Inglês
10.1093/bioinformatics/btw493
ISSN1367-4811
AutoresDmitry Antipov, Nolan Hartwick, Max W. Shen, Mikhail Raiko, Alla Lapidus, Pavel A. Pevzner,
Tópico(s)Antibiotic Resistance in Bacteria
ResumoMotivation: 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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