Ampile

Amplicon pileup analysis pipeline
Current version: v1.2.3

Introduction

• This is Hang's analysis pipeline for amplicon-based mutational profiling.
• The tool calculates absolute mutation rates for each sample.
• For comparative analyses between groups, please perform those manually with the output spreadsheets.

How to setup the environment:

• Install curl if it is not already installed on your system (e.g., sudo apt install curl on Ubuntu).
• Connect to internet and execute the below command in terminal:

bash -c "$(curl -fsSL https://raw.githubusercontent.com/chenh19/Ampile/main/setup.sh)"

How to run the pipeline:

• Prepare reference sequences and sequencing reads in a folder (examples files available).
• Connect to internet and execute the below command in terminal:

bash -c "$(curl -fsSL https://raw.githubusercontent.com/chenh19/Ampile/main/ampile.sh)"

• There is also a simple tutorial for quick reference.