Using abricate to search for antimicrobial resistance genes

I'm learning to use the abricate software for identifying antimicrobial resistance (AMR) genes in bacterial genomes.

Start abricate

First I need to load abricate on the Sanger compute farm (for Sanger users only):

% module avail -t | grep -i abricate 

abricate/1.0.1

% module load abricate/1.0.1

Run abricate

I have a bacterial genome in a file mygenome.fa and want to search for AMR genes in it, using abricate and the NCBI AMR database. Luckily, the NCBI AMR database is on the Sanger farm in the directory /lustre/scratch118/infgen/pathogen/pathpipe/abricate/db, so I can type:

% abricate --datadir /lustre/scratch118/infgen/pathogen/pathpipe/abricate/db --db ncbi mygenome.fa

Say you have lots of files that you want to run abricate on. If you make a file fofn.txt with a single column with a list of the fasta files that you want to run abricate on, you can run abricate on multiple files:

%  abricate --datadir /lustre/scratch118/infgen/pathogen/pathpipe/abricate/db --db ncbi --fofn fofn.txt

Note that abricate can also be used to find virulence genes, e.g. using the vfdb (virulence factor database):

% abricate --datadir /data/pam/software/abricate/db --db vfdb mygenome.fa

Output for abricate 

 The output looks like this:

 #FILE   SEQUENCE        START   END     STRAND  GENE    COVERAGE        COVERAGE_MAP    GAPS    %COVERAGE       %IDENTITY       DATABASE        ACCESSION       PRODUCT RESISTANCE
mygenome.fasta        NODE_11_length_118020_cov_55.534451     70862   71335   +       dfrA1   1-474/474       =============== 0/0     100.00  100.00  ncbi    A7J11_00830     trimethoprim-resistant dihydrofolate reductase DfrA1

 The columns in the output file are described here.

 Note that abricate finds genes that cause antimicrobial resistance, but does not find SNPs that find antimicrobial resistance.

Acknowledgements

Thanks to my colleague Sam Dougan for advice about abricate.