plasmidSPAdes protocols

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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 pipelines

 (2)
2018
PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] shows some portions of large contigs classified as putative plasmids. this may correspond to plasmids with similar coverage to the chromosome, due to low copy number, or to misclassification by plasmidspades., pacbio scaffold sequences were compared against themselves with the bl2seq blastn algorithm [], and act [] was used for synteny visualization. the resulting overlapping sequences […]

2016
PMCID: 5064112
PMID: 27738039
DOI: 10.1128/genomeA.01125-16

[…] 2500 technology (illumina, san diego, ca), and read quality was assessed using fastqc 0.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). these short reads were then assembled using plasmidspades (), which uses the read coverage of generated contigs to distinguish between chromosomal and plasmid dna. the assembly of plasmid contigs rendered a sequence that was 99,874 nucleotides […]


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plasmidSPAdes in publications

 (27)
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] or a1_002_gull) with highly similar core genomes had very different resistance profiles. a total of 61 individual, non-intrinsic amr genes were detected in putative plasmids assembled using plasmidspades, whereas 18 acquired amr genes were not detected in plasmids using this method (fig. )., we compared individual amr gene sequences between isolates, identifying more than one genotype […]

PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] shows some portions of large contigs classified as putative plasmids. this may correspond to plasmids with similar coverage to the chromosome, due to low copy number, or to misclassification by plasmidspades., pacbio scaffold sequences were compared against themselves with the bl2seq blastn algorithm [], and act [] was used for synteny visualization. the resulting overlapping sequences […]

PMCID: 5915459
PMID: 29720977
DOI: 10.3389/fimmu.2018.00790

[…] 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. […]

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

[…] 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 […]

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

[…] 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 […]


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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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