Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S.

Genome Res. 2018 Nov;28(11):1720-1732. doi:10.1101/gr.236273.118

Chromosome assembly of large and complex genomes using multiple references.

Ragout 2 can take multiple reference genomes as input and automatically infers phylogenetic relationship between them. Polymorphisms unique to the target genome can be recovered, but chromosome fusions are typically hard to detect.