PhacoBioIT: A scalable workflow solution for analysis and visualization ultra-low coverage NGS data from Pre-implantation genetic testing for aneuploidy.

Introduction

PhacoBioIT was written by molecular biologist/bioinformatics expert anegin97. PhacoBioIT was created with the hope that other colleagues who are not specialized in using applications that require command line knowledge can perform the PGT-A data analysis process automatically with just the click of a button. The software is deployed as a web application, integrating data visualization tools along with a database to manage sample files.

PhacoBioIT mainly built with python and R, it includes the followings dependencies:

• Flask
• bwa
• samtools
• zip
• unzip
• cnvkit
• ggplot2
• tidyverse
• dplyr
• shiny
• DT
• RSQLite
• ggtext
• dplyr
• plotly
• smoother
• magick
• patchwork
• purrr
• here

Installation

Docker

The pipeline can be installed via Docker as well.

Clone the repository

git clone https://github.com/Anegin24/PhacoBioIT.git
cd PhacoBioIT

Prepare database and index: Download from link: Ref

unzip Ref

Setup docker image:

sudo docker build -t cnvviso -f CNVvisodocker .
sudo docker build -t phacobioit -f dockerfile .

Run docker compose:

In docker-compose.yml, you will see:

bash "directory/DATA:/media/anegin97/DATA/DATA" => Change "directory" to path contain DATA hard disk where store data

bash "directory/PhacoBioIT/CNVdat:/home/anegin97/Bioinformatics/appforclient/CNVdat" => Change "directory" to path contain DATA hard disk where store Rsqlite database

🚀🚀🚀🚀🚀

sudo docker compose up -d

Citation

Huu An, N., Hong Nhung, T. T., Huong, B. B., Quang Tien, V., Dung, P. T., Ngan, N. T., … Hoi, L. T. (2025). PhacoBioIT: A scalable workflow for analysing and visualising ultra-low coverage whole-genome sequencing data in preimplantation genetic testing. Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, 13(1). https://doi.org/10.1080/21681163.2025.2566246