This is a tool which integrates 4 different bioinformatics tools (Sourmash, MLST, AMRFinder, and ABRicate (specifically the PlasmidFinder Database))
Each of these tools have documentation, which can be found in the below links:
- Sourmash: https://sourmash.readthedocs.io/en/latest/
- MLST: https://github.com/tseemann/mlst
- AMRFinderPlus: https://github.com/ncbi/amr/wiki
- ABRicate: https://github.com/tseemann/abricate
Python will also be required on the device that you are using and download instructions can be found at the following link: https://www.python.org
Simply go to the above link and click on the downloads section, and download for your system (MacOS/Windows/etc.)
In order to enter any fasta file into the pipeline, the tools above must be downloaded. The download instructions are found in the documentation listed above. Assuming you have python on your system, use the following command to use the pipeline.
python <path>/pipeline_ver2.py -i <path_to_directory_with_fasta_files>
Alternatively, --input_dir can be used as opposed to -i
Also note that the path must be specified for both the downloaded pipeline and the path to the directory containing the input fasta files
In order to utilize the GUI (app.R), simply alter the file names that are currently there to your filenames. Additionally, you may need to edit some of the column titles to match what is in the code. Once you have made the necessary edits, you can run the app to view and manipulate the graphs that you have produced as per your needs.
Note that the path for your files must be within the same directory as the app.R file.