Improving hifiasm haplotypes for autopolyploid genome assemblies using constraint programming

Actual versions of hifiasm often produce unbalanced haplotype contigs for autopolyploid genome assemblies. Adding a contraint on the distribution of proteins among haplotypes improves haplotype sizes and busco scores balances. Four species were used to benchmark this approach against hifiasm raw results. The script can be downloaded from<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/chklopp/Separate_haplotypes_with_toulbar2">https://github.com/chklopp/Separate_haplotypes_with_toulbar2</ext-link>.