From: Charles Date: Mon, 18 Nov 2019 01:30:57 +0000 (+0900) Subject: Dans l'avion X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=98c6a6a9d258b7225a6d3275cbe9dc343953d6d9;p=source.git Dans l'avion --- diff --git a/biblio/30497373.mdwn b/biblio/30497373.mdwn new file mode 100644 index 00000000..ed899729 --- /dev/null +++ b/biblio/30497373.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies."]] +[[!tag assembly software]] + +Roach MJ, Schmidt SA, Borneman AR. + +BMC Bioinformatics. 2018 Nov 29;19(1):460. doi:10.1186/s12859-018-2485-7 + +Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. + +[[!pmid 30497373 desc="Aligns the reads to the draft genome in order to estimate coverage. A bimodal distribution is expected: the 0.5× peak represents areas where both alleles are present in the assembly."]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index 9d5a0012..d58f2667 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -38,6 +38,10 @@ 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_”. +Purge Haplotigs ([[Roach, Schmidt and Borneman (2018) |biblio/30497373]]) is an +alternative to HaploMerger that takes read coverage into account when detecting +potential haplotigs. + 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. Version