From cf0ac22fc727c78a47727927d3bd96d4bf994470 Mon Sep 17 00:00:00 2001 From: Charles Date: Fri, 1 Mar 2019 13:32:38 +0900 Subject: [PATCH] SALSA --- biblio/28701198.mdwn | 10 ++++++++++ tags/assembly.mdwn | 4 ++++ 2 files changed, 14 insertions(+) create mode 100644 biblio/28701198.mdwn diff --git a/biblio/28701198.mdwn b/biblio/28701198.mdwn new file mode 100644 index 00000000..a853897d --- /dev/null +++ b/biblio/28701198.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Scaffolding of long read assemblies using long range contact information."]] +[[!tag genome assembly software]] + +Ghurye J, Pop M, Koren S, Bickhart D, Chin CS. + +BMC Genomics. 2017 Jul 12;18(1):527. doi:10.1186/s12864-017-3879-z + +Scaffolding of long read assemblies using long range contact information. + +[[!pmid 28701198 desc="Does not require a priori knowledge on the number of chromosomes. Outperforms LACHESIS on noisy data."]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index f1f20f03..9dc13ef5 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -33,6 +33,10 @@ Relase notes of HM2 version 20180603 suggest to use “_HapCUT2 or other phasing tools to get the high-quality haplotype assembly based on the reference haploid 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. + 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. -- 2.47.3