#ABRicate
Mass screening of contigs for antiobiotic resistance genes.
By Torsten Seemann | @torstenseemann | blog
##Quick Start
% abricate 6008.fasta
#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY
Processing: 6008.fna
Found 12 ABR genes in 6008.fna
Klebsiella.fna NC_021232.1 872545 872964 fosA 1-420/420 =============== 0 100.00 100.00
Klebsiella.fna NC_021232.1 1381252 1382427 oqxA 1-1176/1176 =============== 0 100.00 99.32
Klebsiella.fna NC_021232.1 2584899 2585759 blaSHV1 1-861/861 =============== 0 100.00 99.88
##Installation
###Brew If you are using the OSX Brew or LinuxBrew packaging system:
brew tap homebrew/science
brew tap tseemann/homebrew-bioinformatics-linux
brew install abricate
###Source
If you don't use Brew, you will also need to make sure you have BLAST+ installed for blastn.
git clone https://github.com/tseemann/abricate.git
./abricate/bin/abricate --help
##Input
Abricate takes FASTA contig files. It can take multiple fasta files at once!
% abricate ref.fa strains*.fasta /ncbi/Ecoli/*.fna
It does not accept raw FASTQ reads; please see SRTS2 for that.
##Output
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) | ABR gene |
| COVERAGE | 1-1920/1920 | What proportion of the gene is in our sequence |
| COVERAGE_MAP | =============== | A visual represenation |
| GAPS | 0 | Was there any gaps in the alignment - possible pseudogene? |
| %COVERAGE | 100.00% | Proportion of gene covered |
| %IDENTITY | 99.95% | Proportion of exact nucleotide matches |
##Caveats
- Whole codon gaps (3 bp) are still listed as frame-shifts
- Gap reporting incomplete
- Possible coverage calculation issues
##Database
The current database is built from ResFinder.
% abricate --list
aminoglycoside 164
beta-lactamase 1310
colistin 1
fosfomycin 21
fusidicacid 3
macrolide 136
nitroimidazole 14
oxazolidinone 3
phenicol 36
quinolone 103
rifampicin 9
sulphonamide 50
tetracycline 113
trimethoprim 53
vancomycin 124
TOTAL 2140
The raw ResFinder database is processed using the scripts/abricate-fix_resfinder_fasta tool which:
- removes redundant sequences
- re-orients backward sequences
- removes sequences with non-DNA bases
- removes partial coding sequences This could have unexpected consequences on your results and needs to be investigated further with the curators of ResFinder.
##Updating the database
If you don't want to wait for a new release of Abricate you can updated the db folder manually.
# Download and create a new db.XXXXXX folder
cd /path/to/abricate/scripts
./abricate-update_db
# Check it all looks ok
ls -l db.XXXXXX
# Replace the old db folder
mv ../db ../db.old
mv db.XXXXXX ../db
# See if it worked
abricate --list
##Adding your own sequences
There is nothing particularly special about ABRicate - it's just a glorified BLASTN tool.
If you want to add in your own sequences, just add them to the BLASTN database db/resfinder.
The sequence ID that is reported is the FASTA ID,
but stripped to the right after the first underscore '_'.
##Issues
Please report problems here: https://github.com/tseemann/abricate/issues
##License
GPL Version 2: https://raw.githubusercontent.com/tseemann/abricate/master/LICENSE
##Etymology
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.