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Abricate specifications

Information


Unique identifier OMICS_32147
Name Abricate
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Any sequence file that EMBOSS can convert to FASTA files.
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.8.7
Stability Stable
Requirements
BLAST+, EMBOSS
Maintained Yes

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Documentation


Maintainer


  • person_outline Torsten Seemann

Abricate citations

 (11)
library_books

Multidrug Resistant Salmonella enterica 4,[5],12:i: Sequence Type 34, New South UK, Australia, 2016–2017

2018
PMCID: 5875280
PMID: 29553318
DOI: 10.3201/eid2404.171619

[…] enomic similarity and STs by using the Nullarbor pipeline (). We identified antimicrobial resistance (AMR) genes by screening contigs through ResFinder () and CARD (https://card.mcmaster.ca) by using ABRicate version 0.5 (https://github.com/tseemann/abricate). Markers of colistin resistance were examined by using CLC Genomics Workbench (QIAGEN, Valencia, CA, USA). We identified Salmonella 4,[5],12 […]

library_books

A P7 Phage Like Plasmid Carrying mcr 1 in an ST15 Klebsiella pneumoniae Clinical Isolate

2018
Front Microbiol
PMCID: 5786510
PMID: 29403463
DOI: 10.3389/fmicb.2018.00011

[…] uence typing and wzi allele databases of K. pneumoniae available at http://bigsdb.pasteur.fr/klebsiella/klebsiella.html. Antimicrobial resistance genes were identified from genome sequences using the ABRicate program (https://github.com/tseemann/abricate) and ResFinder (https://cge.cbs.dtu.dk/services/ResFinder/). The plasmid carrying mcr-1, designated pMCR_SCKP-LL83, was circularized using PCR an […]

call_split

Comparative genomics identifies distinct lineages of S. Enteritidis from Queensland, Australia

2018
PLoS One
PMCID: 5770046
PMID: 29338017
DOI: 10.1371/journal.pone.0191042
call_split See protocol

[…] MLST was performed in RidomSeqSphere+ 4.1.0 (Ridom, Germany) using the Achtman scheme hosted at Enterobase (https://enterobase.warwick.ac.uk/species/index/senterica) []. AMR genes were detected using Abricate with the ResFinder and CARD databases (https://github.com/tseemann/abricate), and chromosomal point mutations associated with antimicrobial resistance were detected using ResFinder [, ]. The […]

library_books

Cryptic transmission of ST405 Escherichia coli carrying blaNDM 4 in hospital

2018
Sci Rep
PMCID: 5762679
PMID: 29321680
DOI: 10.1038/s41598-017-18910-w

[…] ence to query the multi-locus sequence typing database of E. coli (http://enterobase.warwick.ac.uk/species/index/ecoli). Antimicrobial resistance genes were identified from genome sequences using the ABRicate (https://github.com/tseemann/abricate) program. Plasmid replicon types were determined using by the PlasmidFinder tool at http://genomicepidemiology.org/ and the allele types of IncF plasmids […]

library_books

Translating genomics into practice for real time surveillance and response to carbapenemase producing Enterobacteriaceae: evidence from a complex multi institutional KPC outbreak

2018
PeerJ
PMCID: 5756455
PMID: 29312831
DOI: 10.7717/peerj.4210

[…] in silico as was the presence or absence of antimicrobial resistance (‘resistome’) and other genes (pan-genome) using BLAST-based tools (https://github.com/tseemann/mlst) (https://github.com/tseemann/abricate) (https://github.com/sanger-pathogens/Roary) (). The pan-genome data was imported into FriPan (https://github.com/drpowell/FriPan) for web-browser visualisation using a Python script (https:/ […]

call_split

Methicillin Resistant Staphylococcus aureus Transmission in a Ghanaian Burn Unit: The Importance of Active Surveillance in Resource Limited Settings

2017
Front Microbiol
PMCID: 5635451
PMID: 29056927
DOI: 10.3389/fmicb.2017.01906
call_split See protocol

[…] es 3.9.0 () and mapped to the fully assembled chromosome of S. aureus COL (ST250) (chromosome: CP000046) using snippy v3.2. MLST and antibiotic resistance detection were undertaken with mlst v2.8 and abricate v0.5-dev, respectively. Maximum likelihood Phylogenetic trees were generated using an alignment of core genome SNPs with FastTree v2 () under the GTR model. Trees were visualized using FigTre […]

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