Water Monitor

Code

The code is divided in three folders:

• FALCON-meta
• GOTTCHA2
• Circos
• R_SCRIPTS
• SIMULATED_DATA

Example of use

Example of use

The following steps should be done to analyze your samples:

• 1- Create a profile account at KBase (https://www.kbase.us/) online platform to run the GOTTCHA2 software. The workflow to run GOTTCHA2 for the simulated database from MOSCA can be executed at https://narrative.kbase.us/narrative/128450.
• 2- Install the FALCON-meta algorithm (https://github.com/cobilab/falcon) using ANACONDA (https://www.anaconda.com/, available for all operating system platforms). In Windows the linux subsystem should be installed. All software is open source.
• 3- Run the samples in GOTTCHA2 and FALCON-meta and save the results. FALCON-meta command should be: “./FALCON -v -F -t 15 -l 47 -x output_file.txt transcriptome_example.fasta your_reference_database.fasta”
• 4- Run the R script (MERGE_TABLES_GOTTCHA2-FALCON_script.R) from https://github.com/waterpt/watermonitor to merge the results from both datasets. (R software package should be installed from https://www.r-project.org/)
• 5- Run the CIRCOS script to generate the graphic representation of the detected pathogenetic strains.
• 5- You should obtain a graphic representation similar to next figure:

ISSUES

Please let us know if there is any issues.

LICENSE

License is GPLv3. For more information:

http://www.gnu.org/licenses/gpl-3.0.html