From f5519613fc476f61b8a3eca3f9877fbcab20747e Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Fri, 11 Jan 2019 15:31:41 +0900 Subject: [PATCH] HM2 sub-assemblies are not haplotype-phased. --- tags/assembly.mdwn | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index 10572045..5e269c65 100644 --- 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 -- 2.47.3