Submitted:
15 July 2026
Posted:
16 July 2026
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Abstract
Abricate is a Unix command line bioinformatics tool for screening bacterial genome assemblies for the presence of specific DNA sequences, most commonly antibiotic resistance genes, virulence factors, and genotyping amplicons. Abricate accepts many input sequence formats, optionally compressed, and outputs machine readable tabular reports. Individual reports from different genomes can be combined into a tabular summary report in a presence/absence matrix format. The minimum percentage identity and coverage for a sequence to be reported can be set at runtime. Included are twelve popular databases, and users can create custom databases. Abricate is written in Perl 5 and is available under an open source GPL licence from github.com/tseemann/abricate.
Keywords:
bioinformatics
; bacteria
; genomics
; software
; antimicrobial resistance
Impact Statement
The world’s public sequence databases now contain millions of bacterial genomes. Abricate provides a simple, reliable, and fast way to scan genomes for the presence of particular sequences. Its bundled databases and consistent tabular output format make integration into larger pipelines straightforward.
Data Summary
The source code and documentation for Abricate is available at https://github.com/tseemann/abricate under a GPL 2.0 open source licence, and is installable via the Bioconda in the abricate package.
Introduction
The explosion of high-throughput genomes sequencing has resulted in the deposition of many millions of bacterial genomes into public repositories, with INDSC having more than 3 million bacterial genomes available.
The ability to scan these genomes for particular sequences is a key part of many bioinformatics pipelines. Common classes of sequences searched for are antibacterial resistance genes, virulence factors, toxin genes, genotyping amplicons, and marker genes. Curated databases of these sequences do exist, but are not consistent in their data format, metadata ontology, or method of download.
Here we describe Abricate, a Unix command line bioinformatics tool which can be used to scan bacterial genome assemblies against curated sequence databases. Abricate is a simple linear workflow written in Perl 5 which takes a genome assembly and a choice of 12 bundled databases, and generates a tabular report of identified sequences. These reports can also be combined into summary reports of sequence presence and absence.
Implementation
Input
Abricate requires an assembled genome in FASTA format. However, all input files are filtered through the any2fasta1 tool which converts a variety of common sequence formats into plain FASTA, including any required uncompressing.
Options
Abrivate has no mandatory parameters besides the FASTA input file. However, there are various parameters which can be used to modify its operation. The sensitivity of database sequence matching is controlled with the --mind (minimum % DNA identity match, default 80%) and --mincov (minimum % aligned) database sequence, default 80%). The default output format is TSV with a header row, but can be changed to CSV using --csv and header omitted using --noheader.
Databases
Abricate includes a number of preformatted public databases, which can be listed using the --list command. These include antimicrobial resistance gene databases (NCBI AMR Reference Gene Catalog2, Comprehensive Antibacterial Resistance Database (CARD)3, ResFinder4, ARG-ANNOT5 ,MEGARes6), genotyping databases (EcOH for E.coli serotyping7, PlasmidFinder for plasmid typing8, and virulence factor database (VFDB9, PHAC E.coli Virulence Factors10, UPEC/ExPEC Virulence Factors11, VICTORS12, BacMET13).
Running
The core sequence matching between the query genome sequence and the chosen gene database is performed by BLAST+14 using advanced options including --culling_linit and --max_target_seqs to optimise alignment performance by avoiding too many duplicate matches, as most of the databases have many near-identical sequences. The databases are already pre-indexed into BLAST format at installation time by the --setupdb command in Abricate.
Output
Abricate produces a tabular output with 15 named columns. The first 5 columns (FILE, SEQUENCE, START, END, STRAND) refer to the location on the query genome where the match was found. The 4 columns (DATABASE, ACCESSION, GENE, PRODUCT) describe the source of the sequence match in the database. The match similarly is measured by 5 columns (CoVERAGE, COVERAGE_MAP, COVERAGE%, IDENTITY%, GAPS). A final column is used for database dependent metadata, most commonly (RESISTANCE) for the predicted antimicrobial resistance phenotype.
Summary Mode
Abricate reports can be combined into a summary report using the --summary mode and providing all the output files on the command line. In this mode, the results are transformed into a gene presence/absence matrix, with columns harvested from all the unique matched GENE matches. and rows based on the input FILE name). Each cell in the matrix uses the COVERAGE value of that gene match in that file.
Discussion
Abricate provides a Unix command-line tool for checking for the presence of particular genes in bacterial genome assemblies. The inclusion of 12 popular databases enables uniform analyses to be performed across them. Flexible input support, sensible default parameters, and standard tabular output make integration into larger bioinformatics pipelines trivial.
There is much scope for improvements to Abricate. It currently only supports databases of nucleotide sequences, but could be extended to support amino acid databases by using blastx instead of blastn. Similarly, even with nucleotide databases, the matching and scoring could be performed in amino acid space, as is more standard for antimicrobial resistance gene analysis. More output formats, particularly GFF15 or JSON16, would improve interoperability with other bioinformatics tools and A.I agentic workflows.
Author Contributions
T.S conceived, designed & implemented the software, and wrote the manuscript.
Funding
This research was partially supported by the Victorian Life Sciences Computation Initiative (VLSCI), an funding initiative of the Victorian State Government, Australia.
Institutional Review Board Statement
No genomes were harmed in this stidy.
Acknowledgments
The author would like to thank Finlay Maguire, Björn Grüning, Sam Nicholls, and Boas van der Putten for their pull requests to the Abricate Github repository.
Conflicts of Interest
The author declares there are no conflicts of interest.
References
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