rampart-polio

This pipeline complements RAMPART and continues downstream analysis to consensus level.

Installing

Clone this repository:

git clone https://github.com/aineniamh/rampart-polio.git

Create conda environment and activate it:

cd rampart-polio
conda env create -f environment.yml
conda activate rampart-polio

Running

Create run folder:

mkdir [run_name]
cd [run_name]

Where [run_name] is whatever you are calling todays run (as specified in MinKNOW).

Run RAMPART:

rampart --protocol ../rampart-polio --basecalledPath ~/MinKNOW/data/reads/[run_name]/pass --annotationOptions barcode_set=[native | rapid | pcr | all]

basecalledPath should be set to whereever MinKNOW/guppy is going to write its basecalled files.

Open a web browser to view http://localhost:3000