AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.
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Bioinformatics. 2014 Jun 15;30(12):i319-i328. doi: 10.1093/bioinformatics/btu291.
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.
Bao E, Jiang T, Girke T.