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ABRicate

Mass screening of contigs for antimicrobial resistance or virulence genes.

Is this the right tool for me?

  1. It only supports contigs, not FASTQ reads
  2. It only detects acquired resistance genes, not point mutations
  3. It needs BLAST+ 2.x to be installed
  4. It's written in Perl

If you are happy with the above, then please continue!

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     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

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 --HEAD

Bioconda

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

conda install abricate

Source

If you don't use Brew, you will also need to make sure you have BLAST+ installed for blastn and makeblastdb.

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 Ariba or 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) 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

Caveats

  • 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

Databases

ABRicate comes with some pre-downloaded databases:

You can check what you have installed with the --list command:

% abricate --list

argannot:  1749 sequences -  Mar 17, 2017
card:  2117 sequences -  Mar 18, 2017
ncbibetalactamase:  1557 sequences -  Mar 17, 2017
resfinder:  2130 sequences -  Mar 17, 2017
vfdb:  2597 sequences -  Mar 17, 2017

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

Combining reports across samples

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.fna     8          100.00              100.00  .        100.00   100.00;100.00  100.00   99.91   100.00;100.00  100.00
2.fna     3          .                   .       100.00   .        .              100.00   99.91   .              .

Updating the databases

# force download of latest version
% abricate-get_db --db resfinder --force

# force download of latest version
% abricate-get_db --db resfinder --force

Making your own database

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
% makeblastdb -in sequences -title tinyamr -dbtype nucl -parse_seqids -hash_index

% abricate --list
tinyamr:  173 sequences -  Mar 18, 2017

% abricate --db tinyamr screen_this.fasta

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.

Issues

Please report problems here: https://github.com/tseemann/abricate/issues

License

GPL Version 2: https://raw.githubusercontent.com/tseemann/abricate/master/LICENSE

Author

Torsten Seemann | @torstenseemann | blog