This project is the first module of secureSeq, a suite of secure sequencing analysis tools that is in development.
This code computes Presence/Absence, Differential Abundance, and Alpha Diversity testing over OTU data using garbled circuits.
The paper for this project is available at http://biorxiv.org/content/early/2015/09/02/025999.
Dependencies: FlexSC (https://github.com/wangxiao1254/FlexSC) included as jar in lib/; Java 8 (jdk-1.8, jre-1.8)
To install this code first, clone this repository or download zip.
Then, from the command-line run:
$:./compile.sh
In order to use this code:
-
open two terminal windows
-
in the first terminal, run ./x_GenChiPGP.sh where x can be pc (Pre-compute), naive (Per Feature Naive), or sparse (Per Feature Sparse)
-
in the second terminal, run ./x_EvaChiPGP.sh where x can be pc (Pre-compute), naive_(Per Feature Naive), or sparse (Per Feature Sparse)
-
This produces an output of the program for verification of the correctness of the algorithm and circuit size
-
In order to run the analysis, modify the Config.conf by commenting line 4 MODE VERIFY and uncommenting line 5 MODE REAL. Before running an analysis in REAL mode, it is recommended to check the running time against the results in accuracy/