AMR Summary combines the outputs from ResFinder and MOB-recon to yield reports with strain name, gene name, allele, AMR resistance phenotype, percent identity match to the target sequence, contig name, location prediction (plasmid or chromosomal), and plasmid incompatibility sets.
AMR_Summary can be installed using conda
Skip this step if you have already installed conda
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
bash miniconda.sh -b -p $HOME/miniconda
conda update -q conda
You can now install the AMR_Summary package:
conda install -c olcbioinformatics amr_summary
If you encounter the following error:
PackageNotFoundError: Packages missing in current channels:
You need to add one or more of the following channels to your conda install:
- conda-forge
- bioconda
- olcbioinformatics
To see which channels you currently have:
conda config --show channels
To install the missing channel(s)
conda config --append channels olcbioinformatics
conda config --append channels conda-forge
conda config --append channels bioconda
If you encounter issues with the AMR_Summary package, tests are available to ensure that the installation was successful and your credentials are valid.
You will need to clone this repository and run the tests with pytest:
git clone https://github.com/OLC-Bioinformatics/AMR_Summary.git
cd AMR_Summary
python -m pytest tests/ --cov=amr_summary --cov-config=.coveragec -s -vvv
Note that you can supply absolute (e.g. /home/user/analyses/), tilde slash (e.g. ~/analyses/), or relative paths (e.g. analyses/) for all path arguments
- sequence path: name and path of folder containing sequences to process
- database path: name and path of folder containing ResFinder and MOB-recon databases. Note that you do not need to download these databases; they will be downloaded and initialised as part of the script
- report path: name and path of folder in which reports are to be created. Default is sequence_path/reports
- debug: print debug-level logs to console
- version: print version of AMR_Summary
To process sequence files in FASTA format in the folder ~/Analyses/sequences, using databases in /databases, and place reports in the outputs folder in your current working directory
AMR_Summary -s ~/Analyses/sequences -d /databases -r outputs
To process sequences files in FASTA format in the folder sequences in your current working directory using databases in /home/user/databases, and place reports in the sequences/reports folder in your current working directory, and enable debug-level statements
AMR_Summary -s sequences -d /home/user/databases --debug
usage: AMR_Summary [-h] -s -d [-r] [--debug] [-v]
AMR Summary: a pipeline to identify AMR resistance genes located on plasmids
by combining ResFinder and MOB-recon
optional arguments:
-h, --help show this help message and exit
-s , --sequence_path
Path of folder containing sequence files in FASTA
format to process
-d , --database_path
Path of folder containing ResFinder and MOB-recon
databases. If these databases cannot be located, they
will be downloaded
-r , --report_path Path of folder in which reports are to be created.
Default is sequence_path/reports
--debug Enable debug-level messages to be printed to the
console
-v, --version show program's version number and exit
These outputs have been taken from running the supplied tests. You can see these outputs in the tests/outputs folder if you comment out the final test (test_clean_outputs) located in the file tests/test_amr_summary.py
Outputs from ResFinder yield basic information on the presence of AMR genes in the supplied sequence files
Below is an excerpt from resfinder_blastn.xlsx
Below is the contents of mob_recon_summary.csv
MOB-recon reports contain information on plasmids identified in the supplied sequence files
AMR Summary reports combine the ResFinder and MOB-recon reports
Below is the contents of amr_summary.csv
MIT License
Copyright (c) 2022 Government of Canada
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