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Purge Haplotigs improves the haploid and diploid representations of third-gen sequencing based genome assemblies by identifying and reassigning allelic contigs. The implementation is fast and scales well with large genomes, and it is less likely to over-purge repetitive or paralogous elements compared to alignment-only based methods. The software is available at https: //bitbucket. org/mroachawri/purgeₕaplotigs under a permissive MIT licence.
Roach et al. (Thu,) studied this question.