Bioinformatics. 2014 Jun 15;30(12):i302-9. doi:10.1093/bioinformatics/btu280

Kolmogorov M, Raney B, Paten B, Pham S.

Ragout-a reference-assisted assembly tool for bacterial genomes.

Can accept multiple reference genomes. Decomposes refernces and target in synteny blocks and assemble them in a graph.