From: Charles Date: Thu, 4 Feb 2021 04:17:40 +0000 (+0900) Subject: purge_dups X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=c36dc4f1af8003faeffb0af8211e685688b87419;p=source%2F.git purge_dups --- diff --git a/biblio/31971576.mdwn b/biblio/31971576.mdwn new file mode 100644 index 00000000..f284f5f3 --- /dev/null +++ b/biblio/31971576.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Identifying and removing haplotypic duplication in primary genome assemblies."]] +[[!tag assembly software]] + +Guan D, McCarthy SA, Wood J, Howe K, Wang Y, Durbin R. + +Bioinformatics. 2020 May 1;36(9):2896-2898. doi: 10.1093/bioinformatics/btaa025. + +Identifying and removing haplotypic duplication in primary genome assemblies. + +[[!pmid 31971576 desc="Used by the Vertebrate Genomes Project assembly pipeline. Remaps the reads onto the assembly to evaluate heterozygocity of regions where the genome self-maps to itself, and removes the regions where necessary."]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index a396000b..8d4962e3 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -53,8 +53,11 @@ Purge Haplotigs ([[Roach, Schmidt and Borneman (2018) |biblio/30497373]]) is an alternative to HaploMerger that takes read coverage into account when detecting potential haplotigs. However, it does not merge haplotypes. -`purge_dups`, another alternative tp HaploMerger and Purge Haplotivs, performed -well on Flye 2.5 assemblies ([[Guiglielmoni and coll.,2020|biblio/10.1101_2020.03.16.993428]]). +[`purge_dups`](https://github.com/dfguan/purge_dups) [[Guan and coll., +2020|biblio/31971576]], is another alternative to HaploMerger2. Like Purge +Haplotigs, it does not attempt to merge contigs. `purge_dups` performed well +on Flye 2.5 assemblies ([[Guiglielmoni and +coll.,2020|biblio/10.1101_2020.03.16.993428]]). SALSA (Simple AssembLy ScAffolder, [[Ghurye and coll., 2017|biblio/28701198]]) takes Hi-C data and contigs as input and scaffolds them under the hypothesis