HM2 sub-assemblies are not haplotype-phased.

diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 10572045f9c3d84e323b76041a03b9027bbacc86..5e269c655623e0a356cfe9cc130797eec166200c 100644 (file)
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -8,8 +8,17 @@ 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.
 
-The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a diploid
-assembly and outputs a reference and an alternative assembly for each haplotype.
+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
+available for a locus (often due to haplotype collapsing or the allele is
+simply discarded by the de novo assembler), HM2 puts this allele into both
+sub-assemblies. In the sub-assemblies, the allelic scaffolds are given the same
+scaffold name. Finally, because there are switches between haplotypes in the
+rebuilt haploid sub-assemblies, the sub-assemblies are not haplotype phased._”
+Relase notes of HM2 version 20180603 suggest to use “_HapCUT2 or other phasing
+tools to get the high-quality haplotype assembly based on the reference haploid
+assembly_”.
 
 BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll.,
 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy