PT  - JOURNAL ARTICLE
AU  - Dmitry Antipov
AU  - Nolan Hartwick
AU  - Max Shen
AU  - Mikhail Raiko
AU  - Alla Lapidus
AU  - Pavel A. Pevzner
TI  - plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data
AID  - 10.1101/048942
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 048942
4099  - http://biorxiv.org/content/early/2016/04/17/048942.short
4100  - http://biorxiv.org/content/early/2016/04/17/048942.full
AB  - 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{at}spbu.ru