reference_set_selection_benchmark

This repository consists of the pipeline, as well as references to the data used to obtain the results of the corresponding paper: "Benchmarking the impact of reference genome selection on taxonomic profiling accuracy".

The steps to reproduce the paper results are provided on the github repository (https://github.com/JaspervB-tud/reference_set_selection_benchmark) under workflows. The linked data contains metagenomic reads we simulated (using ART), which in combination with the associated reference genomes (accessions included in Zenodo) can be used to reproduce results in the manuscript. In the manuscript we benchmark the impact of different sequence dereplication techniques on taxonomic profiling performance. We consider multiple datasets with different resolutions to assert whether the impact is resolution dependent.