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, Ecoli_VF and VFDB.
Main tool : ABRicate
Additional tools:
- any2fasta 0.4.2
- ncbi-blast+ 2.9.0
- perl 5.30.0
- bioperl 1.7.7-1
The InsaFlu_220727 database included in this docker build is from GitHub and is described in the epi2me-labs/wf-flu repo.
# list out the available databases
$ abricate --list
DATABASE SEQUENCES DBTYPE DATE
megares 6635 nucl 2022-Nov-16
ecoh 597 nucl 2022-Nov-16
plasmidfinder 460 nucl 2022-Nov-16
resfinder 3077 nucl 2022-Nov-16
ecoli_vf 2701 nucl 2022-Nov-16
ncbi 5386 nucl 2022-Nov-16
card 2631 nucl 2022-Nov-16
argannot 2223 nucl 2022-Nov-16
vfdb 2597 nucl 2022-Nov-16
insaflu 34 nucl 2022-Nov-16
# run ABRicate on an influenza assembly using custom database, saving results to file "irma.abricate.tsv"
$ abricate sample_01.fasta --db insaflu | tee insaflu.abricate.tsv
Using nucl database insaflu: 34 sequences - 2022-Nov-16
Processing: sample_01.fasta
#FILE SEQUENCE START END STRAND GENECOVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE
Found 2 genes in sample_01.fasta
Tip: the abricate manual is at https://github.com/tseemann/abricate/blob/master/README.md
Done.
sample_01.fasta SRR10013255_4 23 1868 + HA 1-1843/1843 ========/====== 1/3 100.00 94.80 insaflu CY018765 CY018765.1 Influenza B virus (B/Yamagata/16/1988) segment 4 complete sequence Yamagata
sample_01.fasta SRR10013255_7 31 1171 + M1 1-1141/1141 =============== 0/0 100.00 96.67 insaflu AF100378 AF100378.1 Influenza B virus B/Yamagata/16/88 segment 7 M1 matrix protein (M) and BM2 protein (BM2) genes complete cds Type_B
# run ABRicate on an assembly supplied with ABRicate code, saving results to file "1.tab"
$ abricate /abricate*/test/assembly.fa | tee 1.tab
Using nucl database ncbi: 5386 sequences - 2022-Oct-13
Processing: /abricate-1.0.1/test/assembly.fa
#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSIONPRODUCT RESISTANCE
Found 5 genes in /abricate-1.0.1/test/assembly.fa
Tip: the --fofn option allows you to feed in a big list of files to run on.
Done.
/abricate-1.0.1/test/assembly.fa LGJG01000038 62416 62796 - blaI_of_Z 1-381/381 =============== 0/0 100.00 95.28 ncbi NG_047499.1 penicillinase repressor BlaI BETA-LACTAM
/abricate-1.0.1/test/assembly.fa LGJG01000038 62786 64543 - blaR1 1-1758/1758 =============== 0/0 100.00 92.83 ncbi NG_047539.1 beta-lactam sensor/signal transducer BlaR1 BETA-LACTAM
/abricate-1.0.1/test/assembly.fa LGJG01000038 64650 65495 + blaZ 1-846/846 =============== 0/0 100.00 96.81 ncbi NG_055999.1 penicillin-hydrolyzing class A beta-lactamase BlaZ BETA-LACTAM
/abricate-1.0.1/test/assembly.fa LGJG01000040 190796 191281 + dfrC 1-486/486 =============== 0/0 100.00 99.59 ncbi NG_047752.1 trimethoprim-resistant dihydrofolate reductase DfrC TRIMETHOPRIM
/abricate-1.0.1/test/assembly.fa LGJG01000041 35416 35844 - fosB-251804940 1-429/429 =============== 0/0 100.00 100.00 ncbi NG_047889.1 FosB family fosfomycin resistance bacillithiol transferase FOSFOMYCIN