AmpliDiff

This repository consists of the source code for AmpliDiff, as well as references to the data used to obtain the results of the corresponding paper: "AmpliDiff: An Optimized Amplicon Sequencing Approach to Estimating Lineage Abundances in Viral Metagenomes".

The steps to reproduce the paper results are provided in the manuscript, and uses the implementation as available on github (https://github.com/JaspervB-tud/AmpliDiff). The linked data contains metagenomic reads we simulated (using ART), which in combination with the associated reference genomes (GISAID identifier EPI_SET_230825gp) can be used to reproduce results in the manuscript. In the manuscript we derive primers and amplicons with our tool to study whether we can replace (idealistic) whole-genome sequencing with targeted amplicon sequencing when profiling metagenomic SARS-CoV-2 reads.