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plasmidSPAdes specifications

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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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  • person_outline Dmitry Antipov

Publication for plasmidSPAdes

plasmidSPAdes citations

 (27)
library_books

Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

2018
Sci Rep
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] tion in the R package ape (v4.1), with different colours representing different alleles. SRST2-detected AMR genes were queried and visualized against putative plasmid contigs that were assembled with PlasmidSPAdes from select isolates using Bandage. Biocide and metal resistance genes were detected from assembled contigs using BacMetScan, using the experimentally confirmed resistance genes dataset […]

library_books

Enterococcus faecalis AHG0090 is a Genetically Tractable Bacterium and Produces a Secreted Peptidic Bioactive that Suppresses Nuclear Factor Kappa B Activation in Human Gut Epithelial Cells

2018
Front Immunol
PMCID: 5915459
PMID: 29720977
DOI: 10.3389/fimmu.2018.00790

[…] BamM v1.7.3 to determine the coverage profiles for each contig. The average coverage was then calculated and contigs with >1,000× coverage were identified as candidate plasmids. In addition, we used PlasmidSPAdes to assemble plasmids from whole genome sequencing data (). The candidate plasmids were manually curated to determine if they could be closed and compared to other plasmids using Blastn. […]

library_books

Draft Genome Sequences of Four Clinical Legionella pneumophila Isolates from Ontario, Canada

2018
Genome Announc
PMCID: 5897800
PMID: 29650583
DOI: 10.1128/genomeA.00295-18

[…] ted using Quast version 4.6.2 (). For the four assemblies, the genome size and G+C contents varied from 3.43 to 3.59 Mb and 38.2 to 38.3%, respectively ().Separately, short reads were assembled using plasmidSPAdes () to identify potential plasmids. We identified a plasmid contig in the LG57 strain. For confirmation, a BAM file including all paired-end reads and the SPAdes assembly graphs were subm […]

library_books

Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn’s disease

2018
PMCID: 5893538
PMID: 29636463
DOI: 10.1038/s41426-018-0065-6

[…] which generated two contigs with the large contig being the chromosome, and the small contig that corresponds to the genome fragment being the plasmid. The plasmid was also consistently identified by plasmidSPAdes. Plasmid identification was performed using bioinformatics tools according to previously described criteria. The criteria defining a plasmid include the presence of ori site containing A […]

library_books

PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data

2018
Microb Genom
PMCID: 5885016
PMID: 29533742
DOI: 10.1099/mgen.0.000164

[…] pe of association is relatively unexplored.Recently a number of methods have been developed to address the problem of assembling mobile genetic elements from next generation sequencing (NGS) data []. plasmidSPAdes[] detects plasmids by analysing the coverage of assembled contigs to separate out chromosomes from plasmid-like sequences. By filtering the dataset, a higher qualityassembly is possible. […]

library_books

Emergence and establishment of KPC 2 producing ST11 Klebsiella pneumoniae in a general hospital in Shanghai, China

2017
PMCID: 5780533
PMID: 29282569
DOI: 10.1007/s10096-017-3131-4

[…] Whole genome sequencing (WGS) was performed with the Illumina HiSeq 2500 system (Illumina, USA). SPAdes (version 3.9.0) was used to assemble the sequences. The plasmid sequences were assembled using plasmidSPAdes (version 3.9.0). Protein function annotation was achieved through BLAST (version 2.2.31+) and HMMER (version 3.1b1). MASH version 1.0.1 was used to compare genes of tested isolates with […]


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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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