Ragout is a tool for reordering contigs to create high quality scaffolds by using a genome rearrangement approach and multiple closely related genome references as a guide. The evolutionary relationship between multiple genome references is used to order contigs. It implements assembly graph and synteny blocks to minimize gaps in assembly.
Sequence assembly
Kolmogorov M, Raney B, Paten B, Pham S "Ragout-a reference-assisted assembly tool for bacterial genomes." Bioinformatics. 2014 Jun 15;30(12):i302-9. https://doi.org/10.1093/bioinformatics/btu280
PMID: 24931998
PMCID: PMC4058940
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