purge_dups

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+[[!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."]]

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@@ -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