plasmidSPAdes pipeline

plasmidSPAdes specifications

Information


Unique identifier OMICS_11489
Name plasmidSPAdes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Dmitry Antipov <>

Publication for plasmidSPAdes

plasmidSPAdes IN pipeline

2017
PMCID: 5381665
PMID: 28391322
DOI: 10.1093/gbe/evx001

[…] of plasmid-borne esx. sequence reads identified as mycobacterium, excluding those belonging to the mtbc or m. leprae, which are not known to harbor plasmids, were downloaded and assembled using plasmidspades v 3.5.0 (antipov et al. 2016). resulting plasmid contigs were annotated using prokka v 1.11 (seemann 2014). plasmids with at least one annotated esx gene were chosen for further quality […]

plasmidSPAdes institution(s)
Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Department of Computer Science and Engineering, University of California, San Diego, USA; Bioinformatics and Systems Biology Program, Massachusetts Institute of Technology, USA
plasmidSPAdes funding source(s)
This study was funded by the Russian Science Foundation [grant 14-50-00069].

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