Job Name (Optional)

A user-defined name to help you identify and organize your analysis results. This name will appear on the results page and is used as the sample name in AMRrules output.

Requirements:

• Maximum 100 characters.
• Allowed characters: letters (A-Z, a-z), digits (0-9), spaces, underscores (_), and hyphens (-).
• Other special characters (e.g. @, !, /) are not allowed.

Select an assembled nucleotide file (-n, --nucleotide)

An assembled nucleotide FASTA file to search. May be gzipped with a .gz extension. This enables AMRFinderPlus to search with translated BLAST, to identify genes and coding point mutations by translated BLAST, frame shifts, and, with the "Organism" option below, non-coding point mutations. Protein HMM searches are not performed if only a nucleotide assembly file is provided.

See the AMRFinderPlus documentation for Input FASTA files.

Select a protein file (-p, --protein)

A protein FASTA file to search. May be gzipped with a .gz extension. This enables the identification of genes and point mutations by BLASTP and genes with HMMs which enables more sensitive and accurate detection of AMR genes without very close homologs in the Reference database. Without a nucleotide assembly AMRFinderPlus will not detect non-coding mutations.

See the AMRFinderPlus documentation for Input FASTA files.

Select a GFF file (-g, --gff)

A GFF3 format file containing gene annotations. This file provides the genomic coordinates and identifiers for the proteins in the nucleotide sequence. If you provide a GFF file, you should also provide the corresponding nucleotide and protein files to enable full AMRFinderPlus functionality.

See the AMRFinderPlus documentation for more details about GFF files and formats.

Annotation Format (--annotation_format)

Specifies the software or pipeline used to generate the gene annotations (GFF and protein files). This is essential for AMRFinderPlus to correctly parse the sequence headers and coordinates when both Protein and Nucleotide files are provided (the recommended way to run AMRFinderPlus). Supported formats include:

• bakta: From the Bakta annotation pipeline.
• prokka: From the Prokka annotation pipeline.
• pgap: From the NCBI Prokaryotic Genome Annotation Pipeline.
• standard: (default) Use for files downloaded from NCBI resources.
• ...and others (genbank, microscope, patric, prodigal, pseudomonasdb, rast).

The AMRFinderPlus documentation for the --annotation_format option contains more information.

Organism group (optional) (-O, --organism)

Specifies the taxonomic group of the organism being analyzed (e.g., Escherichia, Salmonella, Staphylococcus aureus). Providing an organism group allows AMRFinderPlus to use organism-specific curated thresholds and search for point mutations that confer resitance.

If "None" is selected, AMRFinderPlus will perform a general search against its core database of mostly acquired resistance, virulence, and stress genes.

See the AMRFinderPlus documentation for the --organism option.

AMRrules organism (--organism for AMRrules)

Sets the --organism option for AMRrules to interpret the output of AMRFinderPlus using their expert-derived species-specific interpretation rules. This is different from the AMRFinderPlus --organism option. This site has an automatic mapping for some of the commonly used organisms that is used by default, but that automatic mapping may not be correct for your sequences. See the AMRrules supported organism documentation for more information.

File Size and Usage Limits

Because this tool is designed to analyze one bacterial genome at a time, this server has a 10 MB file size limit for each upload. Larger submissions or multiple genomes may fail or be rejected.

Output

Output formats, algorithms, and results are described in the AMRFinderPlus documentation and AMRrules documentation.