abricate

[](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html) [](https://usegalaxy.eu/root?toolid=abricate)

ABRicate

Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, EcoliVF and VFDB, VICTORS, BacMet, UPEC/ExPEC VF.

Is this the right tool for me?

• It only supports contigs, not FASTQ reads
• It only detects acquired resistance genes, NOT point mutations
• It uses a DNA sequence database, not protein
• It needs BLAST+ = 2.7 and any2fasta to be installed
• It's written in Perl :camel:

If you are happy with the above, then please continue! Otherwise consider using Ariba, Resfinder, RGI, SRST2, AMRFinderPlus, etc.

Quick Start

% abricate 6159.fasta
Using database resfinder:  2130 sequences -  Mar 17, 2017
Processing: 6159.fna
Found 3 genes in 6159.fna
#FILE     SEQUENCE     START   END     STRAND GENE     COVERAGE     COVERAGE_MAP     GAPS  %COVERAGE  %IDENTITY  DATABASE  ACCESSION  PRODUCT        RESISTANCE
6159.fna  NC_017338.1  39177   41186   +      mecA_15  1-2010/2010  ===============  0/0   100.00     100.000    ncbi      AB505628   n/a	     FUSIDIC_ACID
6159.fna  NC_017338.1  727191  728356  -      norA_1   1-1166/1167  ===============  0/0   99.91      92.367     ncbi      M97169     n/a            FOSFOMYCIN
6159.fna  NC_017339.1  10150   10995   +      blaZ_32  1-846/846    ===============  0/0   100.00     100.000    ncbi      AP004832   betalactamase  BETA-LACTAM;PENICILLIN

Installation

Bioconda

If you use Conda follow the instructions to add the Bioconda channel:

conda install -c conda-forge -c bioconda abricate
abricate --check
abricate --list

Source

If you install from source, Abricate has the following package dependencies:

• any2fasta for sequence file format conversion
• BLAST+ 2.7.0 for blastn, makeblastdb, blastdbcmd
• Perl modules: LWP::Simple, Bio::Perl, JSON, Path::Tiny
• git, unzip, gzip for updating databases

Most of these are easy to install on an Ubuntu-based system:

sudo apt-get install bioperl ncbi-blast+ gzip unzip git \
  libjson-perl libtext-csv-perl libpath-tiny-perl liblwp-protocol-https-perl libwww-perl
git clone https://github.com/tseemann/abricate.git
./abricate/bin/abricate --check
./abricate/bin/abricate --setupdb
./abricate/bin/abricate ./abricate/test/assembly.fa

Input