AmpliPy

Python implementation of amplicon viral trimming + variant calling + consensus sequence calling, similar to iVar.

Installation

ViralMSA is written in Python 3 and depends on pysam. You can simply download AmpliPy.py to your machine and make it executable:

wget "https://raw.githubusercontent.com/Niema-Lab/AmpliPy/master/AmpliPy.py"
chmod a+x AmpliPy.py
sudo mv AmpliPy.py /usr/local/bin/AmpliPy.py # optional step to install globally

Usage

We will update this section soon 😅

Contributors

• Josh Cross
• Niya Shao
• Ronak Shah
• Niema Moshiri