From: Charles Date: Wed, 20 Nov 2019 03:53:39 +0000 (+0900) Subject: scaffolders... X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=514054ecc965b50055486d92dc036f908daee1b4;p=setup%2F.git scaffolders... --- diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index 450bf877..9f9bd5b6 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -21,13 +21,13 @@ Nagarajan and Šikić, 2017|biblio/28100585]]). When coverage is too low for efficient reference-free assembly, related 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. An -alterative reference-guided assembler, RagOO ([[Alonge and coll., -2019|biblio/31661016]]) is reported to be faster, but can only take a single -reference. +can take multiple reference genomes to guide the scaffolding of a target +assembly. 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. An alterative reference-guided scaffolder, RagOO ([[Alonge and +coll., 2019|biblio/31661016]]) is reported to be faster, but can only take a +single reference. The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a diploid assembly and outputs a reference and an alternative sub-assembly for