ARPA

Automatic RT-PCR Analysis; A tool for massive detection of COVID-19

MOTIVATION

ARPA is designed to help the specialized staff working on the detection of COVID-19 thorugh the technique of RT-PCR. ARPA's main goal is to automatize some laborious steps of the process to speed up the analysis and to decrease the response time.

FUNCTIONALITIES

ARPA has been designed in a modular setting. It allows the automatic analysis of the amplification curves, the visual inspection of the results via a friendly web-interface and the generation of HTML reports with the results from the experiment.

ARPA has several functionalities:

• It generates and analyzes the amplification curves from fluorescence measured in a RT-PCR experiment
• It evaluates the control curves to assess the quality of the experiment
• It evalutes the sample curves to determine the status of each sample
• It provides a friendly web-interface to look at each amplification curve
• It provides a friendly web-interface to look at a summary table with the results of the experiment
• It generates HTML reports with the amplification curves and the status of the plate per each sample

AUTOMATIC ASSESMENT OF THE EXPERIMENT'S QUALITY AND OF THE AMPLIFICATION CURVES

The values of the fluorescence per cycle are retrieved from the files exporteD by the RT-PCR equipment. The curves are evaluated. A correct amplification should behave as a sigmoid curve and cross a fluroescence threshold before a chosen cycle.

• All control samples are evaluated to determine the quality of the experiment.
• The curves for each sample are assesed to determine the status of each sample

FRIENDLY WEB-INTERFACE TO LOOK AT THE AMPLIFICATION CURVES AND THE RESULTS OF THE EXPERIMENT

The web interface allow the user to load the results file generated by the RT-PCR machine

It shows the summary table with the status of each sample of the experiment

It also allow the visual inspection of the amplification curves per sample

Finally, the user can visualize the QC summary table and amplification curves

AUTOMATIC GENERATION OF HTML REPORTS

Individual report (in HTML format) per sample is generated. It contains the amplificacion curves and QC results of the plate.

A quality HTML report with the quality assesment and the control amplification curves is generated

INSTALLATION

• Download the repository

git clone https://github.com/INMEGEN/ARPA.git

You could also download the ZIP file from the download menu in the repository and uncompress the folder

RUNNING ARPA

OPTION 1

• Move to the repository directory

cd ARPA

• Run the installation script. This script will install any required dependencies

sh install.sh

You will be prompted to enter your user password as some commands will do installations as root

• Run ARPA

sh run.R

OPTION 2

• Open RStudio
• Open the app.R file in RStudio
• Click the Run button in Rstudio

TEST DATA

A sample EDS file are provided in the sample_eds directory

AUTHORS

• Laura Gómez-Romero [lgomez@inmegen.gob.mx]
• Guillermo de Anda Jauregui [gdeanda@inmegen.edu.mx ]
• Hugo Tovar [hatovar@inmegen.gob.mx]