Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

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.