New in AMRFinderPlus

AMRFinderPlus 4.0

WARNING: This version has a different database format from versions 1.0-3.12 and is not compatible with those database versions (ie. this is not compatible with database releases before 2024-07-22.1). Run amrfinder -u after installing to download the most recent compatible database version.

Version 4.0 includes StxTyper to accurately type stx operons. We hope to have a manuscript describing this soon.

Because this version includes other software the source installation process has changed. You may have to update your scripts.

A few other changes have been made:

• Filenames have been changed for some of the database files to standardize file extensions. Basically .fa extensions have been added to FASTA files and extensions have been chnaged to .tsv for the tab-delimited files. See AMRFinderPlus database#file-formats for more information.
• The optional hierarchy_node field will now contain two node IDs for fusion proteins and stx operons separated by '::'
• The ability to have different curated blast cutoffs at multiple levels of the hierarchy with the same reference protein has been added
• Output field names have changed as below to make them more uniform across our outputs including MicroBIGG-E:

Field	New name
Protein identifier	Protein id
Contig id	Contig id
Start
Stop
Strand
Gene symbol	Element symbol
Sequence name	Element name
Scope
Element type	Type
Element subtype	Subtype
Class
Subclass
Method
Target length
Reference sequence length
% Coverage of reference sequence	% Coverage of reference
% Identity to reference sequence	% Identity to reference
Alignment length
Accession of closest sequence	Closest reference accession
Name of closest sequence	Closest reference name
HMM id	HMM accession
HMM description
Hierarchy node

WARNING: This version has a different database format from versions 1.0-3.9, and is not compatible with those database versions (Database releases 2018-03-30.1 to 2020-12-17.1). Run amrfinder -u after installing to download the most recent compatible database version.

Note that as of database release 2021-09-30.1 we renamed the fam_id and parent_fam_id to node_id and parent_node_id to maintain consistency with the new node_id, parent_node_id, and hierarchy_node columns of ReferenceGeneHierarchy.txt and ReferenceGeneCatalog.txt.

Upgrading

See Upgrading for instructions on how to update to the latest version of the software and database.

See Installing AMRFinder for help with new installations.

Known issues

• The association between GFF lines and FASTA entries is fragile. AMRFinderPlus works with NCBI produced GFF and protein files, but possibly not others. See the --pgap option to use AMRFinderPlus with annotation files created with PGAP
• Customers installing from the binary distribution have sometimes had linking problems because of glibc versions and libcurl. Please let us know if you have problems. Bioconda installations should avoid these issues.

Usage:

# print a list of command-line options
amrfinder --help 

# Download the latest AMRFinderPlus database
amrfinder -u

# Protein AMRFinderPlus
amrfinder -p <protein.fa> 

# Translated nucleotide AMRFinderPlus
amrfinder -n <assembly.fa>

# protein AMRFinderPlus using GFF to get genomic coordinates
amrfinder -p <protein.fa> -g <protein.gff> 

# search for AMR genes and Campylobacter protein mutations
amrfinder -p <protein.fa> -O Campylobacter 

# Search for everything AMRFinderPlus can find:
# AMR genes, plus genes, protein and nucleotide point mutations, skip blacklisted genes and combine results
amrfinder -p <protein.fa> -g <protein.gff> -n <assembly.fa> -O Campylobacter 

Help

Please open a GitHub issue or email us at [email protected] if you any questions or concerns.