Ragout 2.

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+[[!meta title="Chromosome assembly of large and complex genomes using multiple references."]]
+[[!tag genome chromosome assembly software method]]
+
+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.
+
+[[!pmid 30341161 desc="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."]]

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@@ -8,6 +8,13 @@ Prior assembly, MinIONQC ([[Lanfear and coll., 2018|biblio/30052755]]) allows
 for the comparison of multiple Nanopore runs on the same plot, to assess if
 read length is satisfactory.
 
+When coverage is too low for efficient reference-free assembly, related
+references can be used as a guide.  The Ragout 2 software ([[Kolmogorov and
+coll., 2018|biblio/30341161]]) 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.
+
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a
 diploid assembly and outputs a reference and an alternative sub-assembly for
 each haplotype.  However, they are not phased: “_If only one allele is