From: Charles Plessy Date: Fri, 1 Feb 2019 00:58:41 +0000 (+0900) Subject: Ragout 1. X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=a21b20d387c4cf8c6c6aacab06cea817b536b984;p=source.git Ragout 1. --- diff --git a/biblio/24931998.mdwn b/biblio/24931998.mdwn new file mode 100644 index 00000000..360c2cd7 --- /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 9020cbe9..c0b2a607 100644 --- 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