General Package for State Lab WasteWater Clade Analysis

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Please note this package is being used in conjustion with ClearLabs waste water analysis Workflow should be run after ClearLabs analysis is completed

Clear Labs handles the sequencing and alignment of samples producing BAM files

Quick Start Installation

1. Install necessary conda ENV from WasteWater.yml file in resources

Needed for sucessful analysis

  conda env create -f WasteWater.yaml
  #run to test installing sucessful
  conda activate WasteWater

Before Running update Variables

1. Update necessary locations in Pipeline_Variable.json for your system
2. Check your current version of Chrome and update ChromeDriver to your respective version

This is only needed if downloading results from ClearLabs/other website

Running Workflow

Run Waste Water Analysis

1. Run wasteWater_analysis.py which takes the clear labs run ID as the input

  python wasteWater_analysis.py ClearLabsRunID

See

The package contains the following workflows in their respective subdirectories:

Workflow 0: Scrape_Web

• Navigates to ClearLabs website
• Log in using Private_cache.json file variables located in the data folder
• After logged in the script scrapes run information and downloads BAM, and fastq files

Workflow 1: Freyja Analysis

• Takes BAM files from ClearLabs and runs Freyja
• This will produce a final pdf reports showing lineage break down of samples for given coverage