Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with seven databases: Resfinder, CARD, ARG-ANNOT, NCBI BARRGD, NCBI betalactams, PlasmidFinder and VFDB.
- It only supports contigs, not FASTQ reads (including Genbank and .gz compressed files)
- It only detects acquired resistance genes, not point mutations
- It needs BLAST+ >= 2.2.30 and EMBOSS to be installed
- It's written in Perl
If you are happy with the above, then please continue!
% abricate 6159.fasta
Using database resfinder: 2130 sequences - Mar 17, 2017
Processing: 6159.fna
Found 3 genes in 6159.fna
#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION
6159.fna NC_017338.1 39177 41186 mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 resfinder AB505628
6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169
6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832
If you are using the OSX Brew or LinuxBrew packaging system:
brew tap homebrew/science
brew tap tseemann/bioinformatics-linux
brew install abricate
abricate --check
abricate --setupdb # is done by the installer normally
If you use Conda follow the instructions to add the Bioconda channel:
conda install abricate
abricate --check
abricate --setupdb # is done by the installer normally
If you install from source, Abricate has the following package dependencies:
- BLAST+ for
blastnandmakeblastdb - EMBOSS for
seqret - Decompression tools
gzipandunzip - Perl modules:
LWP::Simple,Text::CSV,Bio::Perl,JSON,File::Slurp
These are easy to install on an Ubuntu-based system:
sudo apt-get install emboss bioperl ncbi-blast+ gzip unzip \
libjson-perl libtext-csv-perl libfile-slurp-perl liblwp-protocol-https-perl libwww-perl
git clone https://github.com/tseemann/abricate.git
./abricate/bin/abricate --check
./abricate/bin/abricate --setupdb
Abricate takes any sequence file that EMBOSS seqret can convert to FASTA files (eg. Genbank,
EMBL), and they can be optionally gzip compressed.
abricate assembly.fa
abricate assembly.fa.gz
abricate assembly.gbk
abricate assembly.gbk.gz
It can take multiple files at once too:
abricate assembly.*
abricate /mnt/ncbi/bacteria/*.gbk.gz
It does not accept raw FASTQ reads; please use Ariba or SRTS2 for that.
Abricate produces a tap-separated output file with the following columns:
| Column | Example | Description |
|---|---|---|
| FILE | Ecoli.fna | The filename this hit came from |
| SEQUENCE | contig000324 | The sequence in the filename |
| START | 23423 | Start coordinate in the sequence |
| END | 24117 | End coordinate |
| GENE | tet(M) | AMR gene name |
| COVERAGE | 1-1920/1920 | What proportion of the gene is in our sequence |
| COVERAGE_MAP | =============== | A visual represenation |
| GAPS | 1/4 | Openings / gaps in subject and query - possible psuedogene? |
| %COVERAGE | 100.00% | Proportion of gene covered |
| %IDENTITY | 99.95% | Proportion of exact nucleotide matches |
| DATABASE | card | The database this sequence comes from |
| ACCESSION | NC_009632:49744-50476 | The genomic source of the sequence |
- Does not find mutational resistance, only acquired genes.
- Gap reporting incomplete
- Sometimes two heavily overlapping genes will be reported for the same locus
- Possible coverage calculation issues
ABRicate comes with some pre-downloaded databases:
- Resfinder
- ARG-ANNOT
- CARD
- NCBI Bacterial Antimicrobial Resistance Reference Gene Database
- NCBI Betalactamase Database
- PlasmidFinder
- VFDB
You can check what you have installed with the --list command.
This lists the available databases in TSV (or CSV with --csv) and three
columns:
% abricate --list
DATABASE SEQUENCES DATE
argannot 1749 2017-Aug-6
card 2153 2017-Aug-6
ncbi 4124 2017-Aug-6
ncbibetalactamase 1557 2017-Aug-6
plasmidfinder 263 2017-Aug-6
resfinder 2228 2017-Aug-7
vfdb 2597 2017-Aug-6
The default database is currently resfinder.
You can choose a different database using the --db option:
% abricate --db vfdb --quiet 6159.fa
6159.fna NC_017338.1 2724620 2726149 aur 1-1530/1530 =============== 0/0 100.00 99.346 vfdb NP_647375
6159.fna NC_017338.1 2766595 2767155 icaR 1-561/561 =============== 0/0 100.00 98.930 vfdb NP_647402
6159.fna NC_017338.1 2767319 2768557 icaA 1-1239/1239 =============== 0/0 100.00 99.677 vfdb NP_647403
6159.fna NC_017338.1 2768521 2768826 icaD 1-306/306 =============== 0/0 100.00 99.020 vfdb NP_647404
6159.fna NC_017338.1 2768823 2769695 icaB 1-873/873 =============== 0/0 100.00 99.542 vfdb NP_647405
6159.fna NC_017338.1 2769682 2770734 icaC 1-1053/1053 =============== 0/0 100.00 98.955 vfdb NP_647406
6159.fna NC_017338.1 2771040 2773085 lip 1-2046/2046 =============== 0/0 100.00 98.778 vfdb NP_647407
ABRicate can combine results into a simple matrix of gene presence/absence.
# Run abricate on each .fa file
% abricate 1.fna > 1.tab
% abricate 2.fna > 2.tab
# Combine
% abricate --summary 1.tab 2.tab
#FILE NUM_FOUND aac(6')-aph(2'')_1 aadD_1 blaZ_32 blaZ_36 erm(A)_1 mecA_15 norA_1 spc_1 tet(M)_7
1.tab 8 100.00 100.00 . 100.00 100.00;100.00 100.00 99.91 100.00;100.00 100.00
2.tab 3 . . 100.00 . . 100.00 99.91 . .
# force download of latest version
% abricate-get_db --db resfinder --force
# re-use existing download and just regenerate the database
% abricate-get_db --db resfinder
Let's say you want to make your own database called tinyamr.
All you need is a FASTA file of nucleotide sequences, say tinyamr.fa.
Idealy the sequence IDs would have the format >DB~~~ID~~~ACC DESC
where DB is tinyamr, ID is the gene name, and ACC is an accession
number of the sequence source. The DESC can be any textual description.
% cd /path/to/abricate/db # this is the --datadir default option
% mkdir tinyamr
% cp /path/to/tinyamr.fa sequences
% abricate --setupdb
% # or just do this: makeblastdb -in sequences -title tinyamr -dbtype nucl -parse_seqids -hash_index
% abricate --list
DATABASE SEQUENCES DATE
tinyamr 173 2017-Aug-28
% abricate --db tinyamr screen_this.fasta
The name "ABRicate" was chosen as the first 3 letters are a common acronym for "Anti-Biotic Resistance". It laso has the form of an English verb, which suggests the tool actual taking "action" against the problem of antibiotic resistance. It is also relatively unique in Google, and is unlikely to receive an infamous JABBA Award.
Please report problems here: https://github.com/tseemann/abricate/issues
GPL Version 2: https://raw.githubusercontent.com/tseemann/abricate/master/LICENSE
Torsten Seemann | @torstenseemann | blog