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.

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.