From ea912bfeb23ff796ffb9e3d6731a80293aa43170 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Thu, 6 Feb 2020 15:55:53 +0900 Subject: [PATCH] dotplot --- biblio/29888139.mdwn | 10 ++++++++++ tags/assembly.mdwn | 4 ++++ 2 files changed, 14 insertions(+) create mode 100644 biblio/29888139.mdwn diff --git a/biblio/29888139.mdwn b/biblio/29888139.mdwn new file mode 100644 index 00000000..eb597467 --- /dev/null +++ b/biblio/29888139.mdwn @@ -0,0 +1,10 @@ +[[!meta title="D-GENIES: dot plot large genomes in an interactive, efficient and simple way."]] +[[!tag software assembly]] + +Cabanettes F, Klopp C. + +PeerJ. 2018 Jun 4;6:e4958. doi:10.7717/peerj.4958 + +D-GENIES: dot plot large genomes in an interactive, efficient and simple way. + +[[!pmid 29888139 desc="Can export to SVG format as well."]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index 268d2911..b999bbb0 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -51,6 +51,10 @@ that most contact points are due to local (same-chromosome) proximity. Version 2 of SALSA uses unitigs and the assembly graph as input ([[Ghurye and coll., 2019|biblio/31433799]]). +Assemblies can be aligned with [[last-dotplot|LAST]] or, for SVG export and +interactive browsing with D-GENIES ([[Cabanettes and Klopp +2018|biblio/29888139]]). + BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll., 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy genes in the assemblies. Seppey, Manni and Zdobnov EM ([[2019|biblio/31020564]]) -- 2.47.3