One recent method that does this is SPRING: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662292/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662292/ Althoug

One recent method that does this is SPRING: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662292/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662292/ Although I'm not familiar with all the details of the method, my understanding is that the reference used by compression can be extremely low quality for biological purposes while still providing good compression -- making it possible to make a quick-and-dirty reference with much less computational time.