Ragout 1.

diff --git a/biblio/24931998.mdwn b/biblio/24931998.mdwn
new file mode 100644 (file)
index 0000000..360c2cd
--- /dev/null
+++ b/biblio/24931998.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ragout-a reference-assisted assembly tool for bacterial genomes."]]
+[[!tag genome assembly chromosome software method]]
+
+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.
+
+[[!pmid 24931998 desc="Can accept multiple reference genomes.  Decomposes refernces and target in synteny blocks and assemble them in a graph."]]

diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 9020cbe992268d521c1187e70c77dd8554c53fe8..c0b2a6070e74b467cb145157da6ae07b3b6134a7 100644 (file)
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -9,11 +9,12 @@ 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.
+references can be used as a guide.  The Ragout software ([[Kolmogorov and
+coll., 2014|biblio/24931998), [[Kolmogorov and coll., 2018|biblio/30341161]])
+can take multiple reference genomes to guide the assembly of one target.
+Polymorphisms unique to the target genome can be recovered, but chromosome
+fusions are typically hard to detect.  Compared to version 1, version 2 infers
+phylogenetic relationships between the reference genomes automatically.
 
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a
 diploid assembly and outputs a reference and an alternative sub-assembly for