### Installation and Verification

Source: https://context7.com/ncbi/amr/llms.txt

Instructions to install and verify the AMRFinderPlus setup, including running the test suite and checking dependencies.

```APIDOC
## Test Installation

### Verify AMRFinderPlus Setup

Run test suite to verify correct installation and database functionality.

```bash
# Download test script
curl -O https://raw.githubusercontent.com/ncbi/amr/master/test_amrfinder.sh

# Test AMRFinderPlus in PATH (bioconda install)
bash test_amrfinder.sh -p

# Test local binary
bash test_amrfinder.sh

# Verify dependencies
blastp -help | head -5
hmmsearch -h | head -5

# Expected success output:
# Success!
```
```

--------------------------------

### Compile and Install AMRFinder

Source: https://github.com/ncbi/amr/wiki/Compile-AMRFinder-from-source

Commands to compile the source code and install the resulting executables. The installation directory can be customized using the INSTALL_DIR variable.

```bash
make
```

```bash
make install
```

```bash
make install INSTALL_DIR=$HOME/amrfinder
```

--------------------------------

### Install Miniconda on Linux

Source: https://github.com/ncbi/amr/wiki/Install-with-bioconda

Downloads and executes the Miniconda installer script for Linux x86_64 systems. Users must follow the interactive prompts to complete the installation and update their shell configuration.

```bash
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash ./Miniconda3-latest-Linux-x86_64.sh
```

--------------------------------

### Verify AMRFinderPlus Installation and Setup

Source: https://context7.com/ncbi/amr/llms.txt

This section details how to verify the correct installation of AMRFinderPlus and its database functionality by running a test suite and checking essential dependencies like BLAST and HMMER. It includes commands for downloading the test script and executing it for both bioconda and local installations.

```bash
curl -O https://raw.githubusercontent.com/ncbi/amr/master/test_amrfinder.sh
bash test_amrfinder.sh -p
bash test_amrfinder.sh
blastp -help | head -5
hmmsearch -h | head -5
```

--------------------------------

### Verify Dependency Installation

Source: https://github.com/ncbi/amr/wiki/Test-your-installation

Checks if BLAST and HMMER binaries are correctly installed and accessible in the system path by invoking their help commands.

```bash
blastp -help
hmmsearch -h
```

--------------------------------

### Install Miniconda on MacOS

Source: https://github.com/ncbi/amr/wiki/Install-with-bioconda

Downloads and executes the Miniconda installer script for MacOS systems. Users must follow the interactive prompts to complete the installation and update their shell configuration.

```bash
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash ./Miniconda3-latest-MacOSX-x86_64.sh
```

--------------------------------

### Install AMRFinderPlus Prerequisites

Source: https://github.com/ncbi/amr/wiki/Install-with-binary

Uses Conda to install the required BLAST, HMMER, and libcurl dependencies in a single command.

```bash
conda install -y blast hmmer libcurl
```

--------------------------------

### Download and Setup AMRFinderPlus Binary

Source: https://github.com/ncbi/amr/wiki/Install-with-binary

Automated script to fetch the latest AMRFinderPlus binary release from GitHub, extract the files, and update the database.

```bash
mkdir amrfinder
cd amrfinder
URL=`curl -s https://api.github.com/repos/ncbi/amr/releases/latest | grep "browser_download_url.*amrfinder_binaries" | cut -d '"' -f 4`
curl -sOL "$URL"
filename=`basename $URL`
tar xvfz $filename
./amrfinder -u
```

--------------------------------

### Install AMRFinderPlus via Bioconda

Source: https://context7.com/ncbi/amr/llms.txt

Sets up a dedicated Conda environment, installs the AMRFinderPlus package, and initializes the required reference database.

```bash
conda create -y -c conda-forge -c bioconda -n amrfinder --strict-channel-priority ncbi-amrfinderplus
source ~/miniconda3/bin/activate amrfinder
amrfinder -u
amrfinder --version
```

--------------------------------

### Install Miniconda on MacOS

Source: https://github.com/ncbi/amr/wiki/BioConda-installation

Downloads and executes the Miniconda installer script for MacOS systems. This script sets up the environment to allow for bioconda package management.

```bash
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOS-x86_64.sh
bash ./Miniconda3-latest-MacOS-x86_64.sh
```

--------------------------------

### Test AMRFinderPlus Custom Database Installation

Source: https://github.com/ncbi/amr/wiki/amrfinder_customize

This command runs a test to verify the correct installation and configuration of the custom database for AMRFinderPlus. It ensures that the database can be built and queried successfully.

```bash
make test_customdb
```

--------------------------------

### Download and Run AMRFinderPlus Tests

Source: https://github.com/ncbi/amr/wiki/Test-your-installation

Downloads the test script from the repository and executes it to verify the installation. The -p flag tests the version currently in the system PATH.

```bash
BASE_URL=https://raw.githubusercontent.com/ncbi/amr/master
curl --silent --location -O ${BASE_URL}/test_amrfinder.sh
bash test_amrfinder.sh -p
```

--------------------------------

### Configure Bioconda Environment

Source: https://github.com/ncbi/amr/wiki/Install-with-binary

Commands to download and install Miniconda and configure the necessary channels for Bioconda to manage software dependencies.

```bash
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash ./Miniconda3-latest-Linux-x86_64.sh
export PATH=$HOME/miniconda3/bin:$PATH
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
```

--------------------------------

### Filter AMRFinderPlus Output by Column Value (Awk)

Source: https://github.com/ncbi/amr/wiki/Tips-and-tricks

This example demonstrates how to filter AMRFinderPlus output using awk based on specific column values. It shows a general pattern for filtering and a specific example for extracting 'core' genes from column 8 or beta-lactam resistance genes from column 11. It requires knowledge of the column number and the value to filter by.

```awk
awk -F'\t' 'NR == 1 || $<column number> == "<value>" { print }' <amrfinder_output>
```

```awk
# filter for beta-lactam resistance elements
awk -F'\t' 'NR == 1 || $11 == "BETA-LACTAM" { print }' test_both.expected
```

--------------------------------

### Install AMRFinder via Conda

Source: https://github.com/ncbi/amr/wiki/BioConda-installation

Installs the ncbi-amr package and all required dependencies using the conda package manager.

```bash
conda install ncbi-amr
```

--------------------------------

### AMRFinderPlus: Print Command-Line Options

Source: https://github.com/ncbi/amr/wiki/New-in-AMRFinderPlus

This command displays a list of all available command-line options for the AMRFinderPlus tool, helping users understand its capabilities and parameters.

```bash
amrfinder --help
```

--------------------------------

### Install AMRFinderPlus via Bioconda

Source: https://github.com/ncbi/amr/wiki/Install-with-bioconda

Creates a dedicated conda environment named 'amrfinder' and installs the ncbi-amrfinderplus package with strict channel priority. This ensures all dependencies are correctly managed.

```bash
source ~/miniconda3/bin/activate
conda create -y -c conda-forge -c bioconda -n amrfinder --strict-channel-priority ncbi-amrfinderplus
```

--------------------------------

### Update AMRFinderPlus

Source: https://github.com/ncbi/amr/wiki/Install-with-bioconda

Updates the existing AMRFinderPlus installation to the latest version available in the configured channels.

```bash
conda update -y -c conda-forge -c bioconda --strict-channel-priority ncbi-amrfinderplus
```

--------------------------------

### Version Information

Source: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus

Prints the software version. Use -V for more complete information.

```APIDOC
## --version

### Description
Print out just the software version. For more complete information, it is recommended to use the `-V` command.

### Method
--version or -v

### Endpoint
N/A (Command-line option)

### Parameters
N/A

### Request Example
```bash
amrfinder.pl --version
```

### Response
N/A (Command-line option)
```

--------------------------------

### List Supported Organisms

Source: https://context7.com/ncbi/amr/llms.txt

Displays all taxa supported for organism-specific point mutation detection and gene filtering.

```bash
amrfinder -l
```

--------------------------------

### GET /reference-gene-hierarchy

Source: https://github.com/ncbi/amr/wiki/AMRFinderPlus-database

Retrieves the hierarchical data structure used for gene identification, including node relationships, symbols, and classification metadata.

```APIDOC
## GET /reference-gene-hierarchy

### Description
Retrieves the tab-delimited hierarchy of genes, families, and upstream nodes used by AMRFinderPlus for identification and naming.

### Method
GET

### Endpoint
/reference-gene-hierarchy

### Parameters
#### Query Parameters
- **scope** (string) - Optional - Filter by 'core' (AMR-specific) or 'plus' (stress/virulence) data subsets.
- **type** (string) - Optional - Filter by protein/mutation type (AMR, STRESS, VIRULENCE).

### Request Example
GET /reference-gene-hierarchy?scope=core

### Response
#### Success Response (200)
- **node_id** (string) - Unique node identifier.
- **parent_node_id** (string) - Identifier for the parent node.
- **symbol** (string) - Gene symbol reported by AMRFinderPlus.
- **hmm_acc** (string) - HMM accession number.
- **scope** (string) - Data subset (core/plus).
- **class** (string) - Broad phenotype definition.
- **subclass** (string) - Specific antibiotic or phenotypic class.

#### Response Example
{
  "node_id": "NG_047348.1",
  "parent_node_id": "NG_047348",
  "symbol": "blaCTX-M-15",
  "scope": "core",
  "type": "AMR",
  "class": "BETA-LACTAM",
  "subclass": "CEPHALOSPORIN"
}
```

--------------------------------

### Upgrade AMRFinderPlus from Source

Source: https://github.com/ncbi/amr/wiki/Upgrading

Commands to pull the latest source code and recompile the software.

```bash
git pull
git submodule update
make clean
make
```

--------------------------------

### Upgrade AMRFinderPlus via Bioconda

Source: https://github.com/ncbi/amr/wiki/Upgrading

Commands to upgrade the AMRFinderPlus package using Conda. Includes standard update and forced version installation.

```bash
source ~/miniconda3/bin/activate
conda update -c conda-forge -c bioconda ncbi-amrfinderplus
conda install -c conda-forge -c bioconda ncbi-amrfinderplus=<version>
```

--------------------------------

### Manage Custom Databases

Source: https://context7.com/ncbi/amr/llms.txt

Commands for using specific database versions, indexing custom directories, and updating the AMRFinderPlus database location.

```bash
amrfinder -p proteins.fa --database /path/to/data/2024-01-31.1
amrfinder_index /path/to/custom/database/2024-01-31.1
amrfinder_update --database /custom/amrfinder/data
```

--------------------------------

### Support for Annotation Formats

Source: https://context7.com/ncbi/amr/llms.txt

Commands demonstrating how to specify the input annotation format when parsing GFF files from different pipelines like Prokka, RAST, Bakta, and PGAP.

```bash
amrfinder -p sample.faa -g sample.gff -n sample.fna --annotation_format prokka
amrfinder -p sample.faa -g sample.gff -n sample.fna --annotation_format rast
amrfinder -p sample.faa -g sample.gff3 -n sample.fna --annotation_format bakta
amrfinder -p annot.faa -g annot.gff -n annot.fna --annotation_format pgap
```

--------------------------------

### AMRFinderPlus: Download Latest Database

Source: https://github.com/ncbi/amr/wiki/New-in-AMRFinderPlus

This command initiates the download of the most recent compatible database for AMRFinderPlus. It is crucial for ensuring accurate and up-to-date analysis, especially after version upgrades.

```bash
amrfinder -u
```

--------------------------------

### Run AMRFinderPlus with Sample Data

Source: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus

This command executes AMRFinderPlus using specified protein and GFF files, along with a DNA FASTA file, and targets a specific organism. It demonstrates the typical command-line interface for the tool.

```bash
amrfinder -p test_prot.fa -g test_prot.gff -n test_dna.fa -O Campylobacter
```

--------------------------------

### Advanced Options

Source: https://context7.com/ncbi/amr/llms.txt

Details on how to configure performance and output for AMRFinderPlus using various command-line options.

```APIDOC
## Advanced Options

### Performance and Output Tuning

Configure threads, identity thresholds, and additional output options.

```bash
# Multi-threaded analysis (default: 4)
amrfinder -n assembly.fa --threads 16

# Custom identity threshold (default: curated or 0.9)
amrfinder -p proteins.fa --ident_min 0.8

# Custom coverage threshold (default: 0.5)
amrfinder -p proteins.fa --coverage_min 0.6

# Report all equally-scoring matches
amrfinder -p proteins.fa --report_all_equal

# Add hierarchy node column to output
amrfinder -p proteins.fa --print_node

# Extract identified proteins to FASTA
amrfinder -p proteins.fa --protein_output identified_proteins.fa

# Quiet mode (suppress status messages)
amrfinder -p proteins.fa -q -o results.tsv

# Custom translation table for BLASTX (default: 11)
amrfinder -n assembly.fa --translation_table 4
```
```

--------------------------------

### AMRFinderPlus Core Usage

Source: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus

Basic command structure for running AMRFinderPlus with required input files.

```APIDOC
## AMRFinderPlus Core Usage

### Description
This section describes the fundamental command-line arguments for running AMRFinderPlus, specifying either protein or nucleotide sequence input.

### Method
Command Line Tool

### Endpoint
`amrfinder (-p <protein_fasta> | -n <nucleotide_fasta>) [options]`

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
`amrfinder -p proteins.fasta`
`amrfinder -n nucleotides.fasta`

### Response
#### Success Response (200)
Output detailing identified AMR genes, their locations, and associated information.

#### Response Example
(Output varies based on input and database)
```

--------------------------------

### Enable Plus Genes and Virulence Factors

Source: https://context7.com/ncbi/amr/llms.txt

Commands to include additional gene categories such as virulence factors, biocide, heat, acid, and metal resistance in the analysis results.

```bash
amrfinder -p proteins.fa --plus
amrfinder -p proteins.fa -g annotation.gff -n assembly.fa -O Escherichia --plus -o results_with_plus.tsv
```

--------------------------------

### Commonly Used Options

Source: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus

Detailed explanation of frequently used command-line options for AMRFinderPlus.

```APIDOC
## Commonly Used Options

### Description
This section details various options available for customizing AMRFinderPlus analysis, including input file types, organism specificity, and output formatting.

### Method
Command Line Tool

### Endpoint
`amrfinder [options]`

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
`amrfinder -p proteins.fasta -g annotation.gff -O Escherichia`
`amrfinder -n genome.fasta --plus`
`amrfinder -V`
`amrfinder -l`

### Response
#### Success Response (200)
Results of the analysis or requested information (e.g., organism list, version info).

#### Response Example
(Varies based on the option used. For `-l`, a list of organisms is printed. For `-V`, version information is printed to STDERR.)

### Options Details:
- `--protein <protein_fasta>` or `-p <protein_fasta>`: Protein FASTA file to search.
- `--nucleotide <nucleotide_fasta>` or `-n <nucleotide_fasta>`: Assembled nucleotide FASTA file to search. Use genomic sequence when running in combined mode.
- `--gff <gff_file>` or `-g <gff_file>`: GFF file for sequence coordinates. Required for combined protein and nucleotide searches. The 'Name=' field in GFF must match protein FASTA identifiers. The first column of GFF must match nucleotide FASTA identifiers.
- `--organism <organism>` or `-O <organism>`: Taxon for screening known resistance-causing point mutations and blacklisting non-informative genes. Use `amrfinder -l` to list possible values.
- `--list_organisms` or `-l`: Prints the list of all possible taxonomy groups for the `-O/--organism` option.
- `--update` or `-u`: Downloads the latest AMRFinderPlus database to the default location.
- `--force_update` or `-U`: Downloads the latest AMRFinderPlus database and overwrites any existing directory.
- `--plus`: Includes results from "Plus" genes such as virulence factors and stress-response genes.
- `--database_version` or `-V`: Prints complete version information for both the database and software. This option should appear alone.
- `--print_node`: Adds an additional "Hierarchy node" column to the output with the node identifier used in the AMRFinderPlus reference gene hierarchy.
```

--------------------------------

### Run amrfinder_customize to Build Custom Database

Source: https://github.com/ncbi/amr/wiki/amrfinder_customize

This command executes the `amrfinder_customize` tool to build or update the AMRFinderPlus database with custom genetic information. It requires input FASTA and metadata files and specifies output database locations.

```bash
amrfinder_customize --database_in data/latest --database_out data/customdb --prot custom.fa --metadata custom.meta
```

--------------------------------

### Run AMRFinderPlus and Combine Results (Bash)

Source: https://github.com/ncbi/amr/wiki/Tips-and-tricks

This script combines the functionality of running AMRFinderPlus on multiple files and then combining their results. It uses a bash loop to process each .assembly.fa file, adding an assembly identifier using the --name option, and then concatenates the results into a combined.tsv file, similar to the previous combination script.

```bash
for assembly in *.assembly.fa
do
    base=$(basename $assembly .assembly.fa)
    # note that we use the --name option to add the "base" as the first
    # column of the output
    amrfinder -n $assembly --threads 8 --plus --name=$base > $base.amrfinder
done

head -1 $(ls *.amrfinder | head -1) > combined.tsv
grep -h -v 'Protein identifier' *.amrfinder >> combined.tsv
```

--------------------------------

### AMR Project Configuration Options

Source: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus

This section outlines the various command-line options available for configuring the AMR project, including parameters for similarity cutoffs, gene coverage, translation tables, and specific pipeline integrations.

```APIDOC
## AMR Project Configuration Options

### Description
This section outlines the various command-line options available for configuring the AMR project, including parameters for similarity cutoffs, gene coverage, translation tables, and specific pipeline integrations.

### Parameters

#### Similarity Threshold
- `--similarity_cutoff <0-1>` or `-s <0-1>`: Minimum similarity proportion for a BLAST-based hit (Methods BLAST or PARTIAL). -1 means use the curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override curated similarity cutoffs. We only recommend using this option if you have a specific reason; don't make our curators sad by throwing away some of their hard work.

#### Minimum Gene Coverage
- `--coverage_min <0-1>` or `-c <0-1>`: Minimum proportion of reference gene covered for a BLAST-based hit (Methods BLAST or PARTIAL). Default value is 0.5

#### Translation Table
- `--translation_table <1-33>` or `-t <1-33>`: Number from 1 to 33 to represent the translation table used for BLASTX. Default is 11. See [Translation table description](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) for a description of the available tables.

#### Pipeline Specific Options
- `--pgap`: Alters the GFF and FASTA file handling to correctly interpret the output of the pgap pipeline. Note that you should use the `annot.fna` file in the pgap output directory as the argument to the `-n/--nucleotide` option.
- `--gpipe_org`: Use Pathogen Detection taxgroup names as arguments to the --organism option.

#### Debugging and Development
- `--parm <parameter string>`: Pass additional parameters to amr_report. This is mostly used for development and debugging.
- `--debug`: Perform some additional integrity checks. May be useful for debugging, but not intended for public use.
```

--------------------------------

### Batch Processing and Matrix Generation

Source: https://context7.com/ncbi/amr/llms.txt

Automate analysis across multiple assembly files and aggregate results into a single file or a presence/absence matrix.

```bash
for assembly in *.assembly.fa; do
    base=$(basename "$assembly" .assembly.fa)
    amrfinder -n "$assembly" --threads 8 --plus --name "$base" > "${base}.amrfinder"
done
head -1 $(ls *.amrfinder | head -1) > combined.tsv
grep -h -v 'Protein identifier' *.amrfinder >> combined.tsv
perl amr2matrix.pl *.amrfinder > matrix.tsv
```

--------------------------------

### Blast Bin Directory

Source: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus

Specifies a directory to search for third-party binaries like blast and hmmer if they are not found in the system's PATH.

```APIDOC
## --blast_bin <directory>

### Description
Specifies a directory to search for 3rd party binaries (blast and hmmer) if they are not in the system's PATH.

### Method
--blast_bin

### Endpoint
N/A (Command-line option)

### Parameters
#### Query Parameters
- **directory** (string) - Required - The path to the directory containing the binaries.

### Request Example
```bash
amrfinder.pl --blast_bin /path/to/blast/bin ...
```

### Response
N/A (Command-line option)
```

--------------------------------

### Run Combined Protein and Nucleotide Analysis

Source: https://context7.com/ncbi/amr/llms.txt

Executes a comprehensive analysis using both protein and nucleotide inputs, with support for specific annotation formats and sample labeling.

```bash
amrfinder -p proteins.fa -g annotation.gff -n assembly.fa -O Escherichia --plus -o results.tsv
```

--------------------------------

### AMRFinderPlus Advanced Options: Performance and Output Tuning

Source: https://context7.com/ncbi/amr/llms.txt

This snippet demonstrates various command-line options for AMRFinderPlus to customize analysis performance and output format. It covers multi-threaded analysis, custom identity and coverage thresholds, reporting all equally-scoring matches, adding hierarchy nodes, extracting identified proteins, enabling quiet mode, and specifying custom translation tables.

```bash
# Multi-threaded analysis (default: 4)
amrfinder -n assembly.fa --threads 16

# Custom identity threshold (default: curated or 0.9)
amrfinder -p proteins.fa --ident_min 0.8

# Custom coverage threshold (default: 0.5)
amrfinder -p proteins.fa --coverage_min 0.6

# Report all equally-scoring matches
amrfinder -p proteins.fa --report_all_equal

# Add hierarchy node column to output
amrfinder -p proteins.fa --print_node

# Extract identified proteins to FASTA
amrfinder -p proteins.fa --protein_output identified_proteins.fa

# Quiet mode (suppress status messages)
amrfinder -p proteins.fa -q -o results.tsv

# Custom translation table for BLASTX (default: 11)
amrfinder -n assembly.fa --translation_table 4
```

--------------------------------

### Perform Nucleotide Sequence Analysis

Source: https://context7.com/ncbi/amr/llms.txt

Analyzes assembled nucleotide FASTA files using translated BLASTX, supporting multi-threading and nucleotide sequence extraction.

```bash
amrfinder -n assembly.fa -O Campylobacter --threads 8 --nucleotide_output identified_regions.fa
```