Overview
This repository provides a hybrid automation pipeline for high-throughput analysis of Sanger sequencing chromatogram files (.ab1) generated from CRISPR/Cas9-edited plant lines.
Gear Genomics INDIGO Webserver (web-based deconvolution & alignment)
ICE (Inference of CRISPR Edits) – local fallback analysis engine
Selenium WebDriver automation
Biopython-based validation
Automated CSV reporting
Advanced logging and structured error handling
This Version 2 hybrid system ensures maximum reliability, accuracy, and scalability by automatically routing failed INDIGO analyses to ICE as a fallback.
Required Python Packages
pip install selenium pandas biopython
ICE must be locally cloned and referenced via:
ice_source_path = r"path_to_ice-master" Citation
If you use this hybrid automation system, please cite:
Suresh, V., Girish, C., & Tavva, V.S.S. Python-based automation of INDIGO webserver using Selenium for high-throughput analysis of CRISPR-induced allelic variations. bioRxiv (2025).**
Contact
Dr. V. S. Sresty Tavva
Tata Institute for Genetics and Society (TIGS)