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 Acinetobacter Plasmid Typing database included in this docker build is v1.0.0 from GitHub and is described in a preprint. The database contains variants of the plasmid rep gene found in Acinetobacter baumannii, as described in the manuscript. When rep genes match with > 95 % identity, this represents a typing scheme for Acinetobacter baumannii plasmids.
The database (FASTA file) has been modified slightly to conform to ABRicate requirements. Lowercase nucleotide sequences a,t,c,g have been converted to uppercase A,T,C,G and FASTA headers were altered according to directions here: https://github.com/tseemann/abricate#making-your-own-database
# list out the available databases
$ abricate --list
DATABASE SEQUENCES DBTYPE DATE
card 2631 nucl 2022-Oct-13
ncbi 5386 nucl 2022-Oct-13
vfdb 2597 nucl 2022-Oct-13
megares 6635 nucl 2022-Oct-13
ecoli_vf 2701 nucl 2022-Oct-13
argannot 2223 nucl 2022-Oct-13
ecoh 597 nucl 2022-Oct-13
plasmidfinder 460 nucl 2022-Oct-13
resfinder 3077 nucl 2022-Oct-13
AcinetobacterPlasmidTyping 152 nucl 2022-Oct-13
# run ABRicate on an A. baumannii assembly using custom database, saving results to file "a-baum-plasmid.abricate.tsv"
$ abricate SAMN19774594_contigs.fasta --db AcinetobacterPlasmidTyping | tee a-baum-plasmid.abricate.tsv
Using nucl database AcinetobacterPlasmidTyping: 152 sequences - 2022-Oct-13
Processing: SAMN19774594_contigs.fasta
#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSIONPRODUCT RESISTANCE
Found 2 genes in SAMN19774594_contigs.fasta
Tip: the --fofn option allows you to feed in a big list of files to run on.
Done.
SAMN19774594_contigs.fasta contig00028 28950 30125 + rP-T1 1-1176/1176 =============== 0/0 100.00 100.00 AcinetobacterPlasmidTyping CP001922.1_ABKp1 rP-T1
SAMN19774594_contigs.fasta contig00059 2896 3831 + r3-T4 1-936/936 =============== 0/0 100.00 100.00 AcinetobacterPlasmidTyping AY541809.1_pMAC r3-T4
# 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