From 06ee90f7fc0ea0c987e518b019e23c3a3a9e6816 Mon Sep 17 00:00:00 2001 From: Charles Date: Tue, 5 Mar 2019 13:18:57 +0900 Subject: [PATCH] SALSA2 --- biblio/10.1101_261149.mdwn | 10 ++++++++++ tags/assembly.mdwn | 4 +++- 2 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 biblio/10.1101_261149.mdwn diff --git a/biblio/10.1101_261149.mdwn b/biblio/10.1101_261149.mdwn new file mode 100644 index 00000000..cf7b5e55 --- /dev/null +++ b/biblio/10.1101_261149.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Integrating Hi-C links with assembly graphs for chromosome-scale assembly"]] +[[!tag genome assembly method]] + +Jay Ghurye, Arang Rhie, Brian P. Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M. Phillippy, Sergey Koren + +bioRxiv, first February 07, 2018. + +Integrating Hi-C links with assembly graphs for chromosome-scale assembly + +[[!doi 10.1101/261149 desc="Uses unitigs and the assembly graph as input."]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index 9dc13ef5..17773727 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -35,7 +35,9 @@ assembly_”. SALSA (Simple AssembLy ScAffolder, [Ghurye and coll., 2017|biblio/28701198]]) takes Hi-C data and contigs as input and scaffolds them under the hypothesis -that most contact points are due to local (same-chromosome) proximity. +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., +2018|biblio/10.1101_261149]]). BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll., 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy -- 2.47.3