This package contains the basic scripts used to screen COVID-19 samples via group testing, as described in the manuscript "Efficient high throughput SARS-CoV-2 testing to detect asymptomatic carriers", by Shental et al.
The protocol allows screening 384 samples using 48 pools, where each sample appears in six pools according to a Reed-Solomon error-correcting code.
Pools should be prepared using a liquid handling robot.
As an example, the "robotRelatedFiles" directory provides the programming code for a Arise Ezmate-601 robot, and an experimental protocol: "Protocol for 48 pools from 384 samples_.docx".
Simple text files describing pooling design appear in the "ExpData" directory.
A Matlab code is provided. In the coming days we would add a standalone version.
The directory "mFiles" contains the relevant files. We provide an example code for analyzing results from an experiment in which two positive carriers in the 384 samples.
PCR results appear in the file "ExpData/ExpTwoCarriersResults.xlsx" providing the C(t) values of each pool.
Follow the lines in "example_PBEST.m" file, or simply run the code, to reconstruct the carriers.
The file contains the following parts:
a) Load the experimental data and the Reed-Solomon (RS) measurement matrix, M.
b) Load the PCR results.
c) Detect the carriers
Acknowledgements: These scripts use a specific file taken from the GPSR package (relevant file included). We thank the Mario Figueiredo for allowing us to include this file in our package.
Please send any comments/bug reports to:
Noam Shental, shental@openu.ac.il
Tomer Hertz, thertz@post.bgu.ac.il