Why not replace the human genome with it's decoy genome version? > < > > < The decoy genome is an improved human genome from the regular reference. It's faster for mapping and it reduces false positive rate. In this case, there shouldn't be any reason to use the regular human reference, because the decoy genome is simply better and faster. For instance, it has DNA sequence for common virus genomes presented in humans. It has everything in the regular reference. **Q:** What's the point of the regular human reference (e.g. hg38) if the decoy version is more accurate and is a better representation for the human variation.

To clarify, when you say "decoy genome" you hopefully mean the decoy genome _and_ the reference genome together; the decoy genome itself is not a complete reference, but a collection of contigs assembled from reads that didn't map to the current reference genome, but are known to be human sequence.

The decoy genome certainly seems to be a useful supplementary data set for speeding up read mapping to the human genome but it cannot be _better_ than the reference because it is not comparable to the reference.