plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data

By Dmitry Antipov, N. Hartwick, Max W. Shen, M. Raiko, Alla L. Lapidus, Pavel A. Pevzner. bioRxiv, 2016

493 citations recorded by the source corpus.

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

Subfields: Ecology, Molecular Biology, Molecular Medicine

View Paper: https://www.semanticscholar.org/paper/5bcbf2ec563cfcde806e0ab6e0773519e3f5de75

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Citations in the corpus

• Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family (2019, unknown): “with plasmidSPAdes [6] using default settings.”
• Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters! (2017, background): “SPAdes [35] was originally developed for single cell sequencing data, but has since grown into a veritable program suite for various applications and data types [35– 38].”