KmerFinderJS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool KmerFinderJS
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Tool usage distribution map

This map represents all the scientific publications referring to KmerFinderJS per scientific context
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Associated diseases

This word cloud represents KmerFinderJS usage per disease context
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Popular tool citations

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Protocols

KmerFinderJS specifications

Information


Unique identifier OMICS_10776
Name KmerFinderJS
Alternative name KmerFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Javascript
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Requirements
Redis
Maintained Yes

Subtool


  • Redis

Download


download.png
bitbucket.png

Versioning


No version available

Maintainer


  • person_outline Mette V. Larsen

Additional information


Previous versions: https://cge.cbs.dtu.dk//services/KmerFinder/ https://bitbucket.org/genomicepidemiology/kmerdb

Information


Unique identifier OMICS_10776
Name KmerFinderJS
Alternative name KmerFinder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Subtool


  • Redis

Maintainer


  • person_outline Mette V. Larsen

Additional information


Previous versions: https://cge.cbs.dtu.dk//services/KmerFinder/ https://bitbucket.org/genomicepidemiology/kmerdb

Publications for KmerFinderJS

KmerFinderJS citations

 (15)
library_books

Aeromonas caviae mimicking Vibrio cholerae infectious enteropathy in a cholera endemic region with possible public health consequences: two case reports

2018
PMCID: 5857081
PMID: 29548295
DOI: 10.1186/s13256-018-1603-5

[…] nline services at the Centre for Genomic Epidemiology of Danish Technical University (https://cge.cbs.dtu.dk/services/). The pipeline successively performed: identification of species from raw reads (KmerFinder 1.1); de novo genome assembly and quality assessment (SPAdes 3.5, Quast 2.3); 16S rRNA species typing (SpeciesFinder 1.2); multi-locus typing (MLST 1.8); and antimicrobial resistance predic […]

library_books

Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples

2018
Genes
PMCID: 5793167
PMID: 29300319
DOI: 10.3390/genes9010014

[…] uence, as well as markers and antibiotic resistance genes. In a study published in 2017 by Joensen et al. [], 55 clinical fecal samples and 10 healthy control samples were analyzed using the software KmerFinder [,] and MGmapper []. The relative abundance of an organism was calculated as the percentage of the total reads in the sample assigned to that organism. The relative abundance of the pathoge […]

library_books

Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr 1 gene indicates bacterial diversity but plasmid restriction

2017
Sci Rep
PMCID: 5681592
PMID: 29127343
DOI: 10.1038/s41598-017-15539-7

[…] in online databases were requested from their respective authors. The quality of the raw sequence reads was checked using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), quast and KmerFinder 2.0 (https://cge.cbs.dtu.dk/services/KmerFinder/) (see Supplementary Methods for more details). Reads were trimmed using Trimmomatic V0.33. De-novo genome assembly was performed with SPAdes […]

call_split

Epidemiology of Extended Spectrum β Lactamase Producing E. coli and Vancomycin Resistant Enterococci in the Northern Dutch–German Cross Border Region

2017
Front Microbiol
PMCID: 5633748
PMID: 29051750
DOI: 10.3389/fmicb.2017.01914
call_split See protocol

[…] also uploaded to the Center for Genomic Epidemiology to extract information on resistance genes (ResFinder) and virulence factors (VirulenceFinder), and species confirmation for VRE and ESBL-E. coli (KmerFinder), and serotype (SerotypeFinder) and plasmid replicons (PlasmidFinder) for ESBL-E. coli (; ; ; , ; ). […]

library_books

Identification of nonserotypeable Shigella spp. using genome sequencing: a step forward

2017
PMCID: 5674244
PMID: 29134117
DOI: 10.4155/fsoa-2017-0063

[…] th any known Shigella sequences in the PATRIC database, which could be due to limitations inherent to the database. However, the rest of the isolates showed similar results to those of SpeciesFinder, KmerFinder and gyrB sequence analysis methods.Five isolates (FC13–FC17) was identified as S. dysenteriae through manual comparison of O-antigen using PATRIC but were misidentified as S. boydii by the […]

library_books

A severe transmissible Majocchi's granuloma in an immunocompetent returned traveler

2017
PMCID: 5502794
PMID: 28725545
DOI: 10.1016/j.mmcr.2017.07.003

[…] European Nucleotide Archive (ENA) in project PRJEB19281 http://www.ebi.ac.uk/ena/data/view/PRJEB19281. Identification as Trichophyton interdigitale was confirmed by a Kmer search on fastq reads using KmerFinder 2.0 (https://cge.cbs.dtu.dk/services/KmerFinder/).The ITS regions 1 and 2 were identified from the de novo assembly and aligned to ITS sequences representing all known Trichophyton interdig […]


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KmerFinderJS institution(s)
National Food Institute, Technical University of Denmark, Lyngby, Denmark; Systems Biology, Technical University of Denmark, Lyngby, Denmark; Hvidovre Hospital, Hvidovre, Denmark

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