This snakemake-based pipeline is an integrated software to predict AMR phenotypes (Resistant / Susceptible), based on PhenotypeSeeker 0.7.3, Kover 2.0, and ResFinder 4.0, for 78 species-antibiotic combinations. Recommendation software for each species-antibiotic combination is based on our benchmarking work.
- Linux (tested version: AlmaLinux 8.5 )
- Conda (tested version: Miniconda2 4.8.4), Snakemake (7.25.0)
- C++/11 capable compiler (e.g. gcc 4.7+, clang 3.5+, Apple/clang 6.0+), see DSK
- CMake 3.1+, see DSK
bash install/install.sh
The input file is a yaml file Config.yaml at the root folder where all options are described:
A. Sample information
Please specify samples' information in sample.txt , where each row contains a strain's sample name, path to genome, and strain species, respectively, separated by a space.
B. Parameters setting
| option | action | values ([default]) |
|---|---|---|
| dryrun | Y or N | N |
| output_path | To where to generate the Results folder for the direct results of each software and further visualization. |
./ |
| log_path | To where to generate the log folder for the intermediate files. |
./ |
| n_jobs | CPU cores to use. | 1 |
| folds_setting | Phylogeny background.Can be one of: close, low_similarity, distant_phylo | close |
| Software | Can be one or multiple (separated by ",") of: PhenotypeSeeker, Kover, ResFinder | ResFinder |
bash main.sh
Example:
<path_to_results>/results
├── sample_txt1
│ ├── Escherichia_coli_kover_close_result.txt
│ ├── Escherichia_coli_phenotypeseeker_close_result.txt
│ └── Escherichia_coli_resfinder_result.txt
└── sample_txt2
├── Escherichia_coli_kover_close_result.txt
├── Escherichia_coli_phenotypeseeker_close_result.txt
└── Escherichia_coli_resfinder_result.txt
-
DSK https://github.com/GATB/dsk accessed on April 2024
-
ResFinder 4.0 https://bitbucket.org/genomicepidemiology/resfinder/src/master/ accessed on May 2021
MIT License
- Open an issue in the repository.
- Send an email to Kaixin Hu ([email protected]).