From c46fcf5576017c0ae712ce3906c353e9957f2315 Mon Sep 17 00:00:00 2001 From: Charles Date: Fri, 4 Sep 2020 13:34:04 +0900 Subject: [PATCH] =?utf8?q?Caf=C3=A9?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- biblio/25940625.mdwn | 10 ++++++++++ tags/assembly.mdwn | 3 +++ 2 files changed, 13 insertions(+) create mode 100644 biblio/25940625.mdwn diff --git a/biblio/25940625.mdwn b/biblio/25940625.mdwn new file mode 100644 index 00000000..4e6edbf0 --- /dev/null +++ b/biblio/25940625.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Accurate identification of centromere locations in yeast genomes using Hi-C."]] +[[!tag assembly software]] + +Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS. + +Nucleic Acids Res. 2015 Jun 23;43(11):5331-9. doi:10.1093/nar/gkv424. + +Accurate identification of centromere locations in yeast genomes using Hi-C. + +[[!pmid 25940625 desc="Tested on yeast and Plasmodium falciparium. First, detects regions enriched in Hi-C contacts. Then, prioritises local maxima enriched in trans-contacts."]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index b999bbb0..259f50eb 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -51,6 +51,9 @@ 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]]). +The Hi-C data can also be used to call the location of centromeres ([[Varoquaux +and coll., 2015|biblio/25940625]], Marie-Nelly and coll., 2014(not read)). + Assemblies can be aligned with [[last-dotplot|LAST]] or, for SVG export and interactive browsing with D-GENIES ([[Cabanettes and Klopp 2018|biblio/29888139]]). -- 2.47.3