bifrost_amrfinderplus

s This component is used to find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences. The component is limited to a predefined set of species native to the utilized tool (described below).

Requirements

• The component uses data which is either an uploaded assembled sequence (event data), which has been filtered through one component, or using the generated de novo assembly from the component
• The component uses the NCBI Antimicrobial Resistance Gene Finder tool AMRfinderplus.
• The versions are described in the environment.yaml
• The AMRfinderplus tool performs species-specific analysis to optimize organism-specific results on a defined set of organisms. If the dataset is uploaded assemblies, the provided species is used as an option for the tool, whereas the de novo generated assembly data utilize the species determined from another component.

Download

git clone https://github.com/ssi-dk/bifrost_amrfinderplus.git
cd bifrost_amrfinderplus
git submodule init
git submodule update
bash install.sh -i LOCAL
conda activate bifrost_amrfinderplus_vx.x.x
export BIFROST_INSTALL_DIR='/your/path/'
BIFROST_DB_KEY="/your/key/here/" python -m bifrost_amrfinderplus -h

Run the snakemake analysis

Each component can be run on a single sample using a single snakemake command, replacing the string passed to the --config sample_name=" " with the appropriate dataset name. The provided component_name= takes as an argument <component_name>__<version_number>. The component name aligns with the GitHub repo name, which is structured like bifrost_<component_name> (e.g. bifrost_amrfinderplus -> component name amrfinderplus), and the version number aligns with the current GitHub tag / or conda environment version (e.g. v.1.0.0) defined during the bifrost component setup.

snakemake -p --nolock --cores all -s <github path>/pipeline.smk --config sample_name="insert sample name" component_name=amrfinderplus__v1.0.0 --rerun-incomplete

Add a species

The inferred species from a different component needs to be mapped to a format specified by the amrfinderplus parameter -O. To add species to this component, the dictionary amrfinderplus_organism_option in file config.yaml needs to be opdated, with the key's fitting the inferred species name, and the value fitting the AMRfinderplus organisms.