abricate

Scan contigs for antimicrobial resistance and virulence genes

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Find antimicrobial resistance and virulence genes in contigs

abricate

Scan a FASTA file for resistance genes using default database$ abricate contigs.fasta > results.txt

Scan with specific database (ncbi, card, resfinder, etc.)$ abricate --db card contigs.fasta > resistance_results.txt

Scan multiple files and generate summary report$ abricate *.fasta | abricate --summary > summary.txt