WAVES (Web-based tool for Analysis and Visualization of Environmental Samples)

A web application for visualization of wastewater pathogen sequencing results

This web-based application enables interactive visualization and analysis of SARS-CoV-2 sequencing data from wastewater treatment plants. The application can be easily customized through the configuration file. For customization of the configuration file you will need a geojson file containing shape of your catchment areas, a csv file containing basic information about catchment areas and sequencing data in the csv table. The software is written in python 3.8 and the web server runs on Plotly Dash.

Quickstart

• git clone https://github.com/ptriska/WavesDash
• cd WavesDash
• pip install -r requirements
• python app.py
• open browser at localhost:8050

Production deployment with Docker

Using image from Docker hub

• docker pull wasa000/waves
• docker run -p [your port]:8050 wasa000/waves

Provide own config file and data

• docker run -p [your port]:8050 --mount type=bind,source=/[path to your config file at local machine]/config.py,target=/home/WavesDash/config.py -v [path to the data folder]/data/:/home/WavesDash/data/ wasa000/waves

Example

Demo verison of the application: https://wavesdashboard.azurewebsites.net/

Customization of the app

• customize the config.py
• supply own data files (example data files are in data/)
• input data file format is described in file_format.txt
• supply own geojson file with sampling areas
• supply own description of sampling locations (sampling_locations.tsv)

Input data file formats

variant data file (data/variant_freq.tsv, tab-delimited)

columns:

• variant (string) name of the variant (e.g. BA.1)
• LocationID (string) ID of the sampling area
• LocationName (string) plain text name of the sampling area
• sample_id (string) ID of the sample
• sample_date (string, YYYY-MM-DD) sampling date
• value (float between 0 and 1) frequency of detected variant in the sample

allele data (data/allele_freq.tsv, tab-delimited)

columns:

• sample_id (string) must correspond to the Sample_ID in the variant frequency file
• position (integer) position in the genome
• chrom (string) genomic feature ID (reference seq ID)
• ref (string) reference allele
• alt (string) alternative allele
• ann_effect (["missense_variant","synonymous variant"]) effect of the mutation
• ann_aa (string) amino acid change caused by the mutation
• allele_freq (float between 0 and 1) frequency of the allele in the sample
• depth (integer) optional; depth of sequencing at the position of the allele