RT Journal Article
SR Electronic
T1 plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 048942
DO 10.1101/048942
A1 Dmitry Antipov
A1 Nolan Hartwick
A1 Max Shen
A1 Mikhail Raiko
A1 Alla Lapidus
A1 Pavel A. Pevzner
YR 2016
UL http://biorxiv.org/content/early/2016/04/15/048942.abstract
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.