Abundance estimation with the use of environmental samples has been used during the SARS-CoV-2 pandemic to identify the abundances of different lineages. AmpliDiff, an algorithm that tries to find parts of DNA that can differentiate between different input genomes was used on a SARS-CoV-2 dataset to find these amplicons. The AmpliDiff algorithm was able to run on the SARS-CoV-2 set but seemed infeasible for datasets that contain larger or more complex genomes because of the computational requirements and runtime. We introduce a new pre-processing strategy based on selecting the most differentiable coding regions and show the modifications done to AmpliDiff to make AmpliDiff work following this new method. Based on the results we conclude that the approach is promising but still requires more research to be used optimally.