One of the problems I encounter when assembling eukaryotic genomes are haplotypic duplications. Simply put, haplotypic duplications are the cases when an assembler mistakenly assembles alleles as paralogs. To deal with this problem, I created a tool Mabs which works as a parameter optimizer of genome assemblers Hifiasm and Flye. In short, it creates a series of assemblies by Hifiasm or Flye and finds the one where BUSCO genes are assembled most accurately. A slightly more detailed description of Mabs can be found on GitHub (https://github.com/shelkmike/Mabs) and a much more detailed in the preprint (https://www.biorxiv.org/content/10.1101/2022.12.19.521016v2). In my experience, Mabs usually creates better or at least equal assemblies compared to Hifiasm and Flye when they are run with their default parameters. This program may be especially useful to those who assemble highly heterozygous genomes, since their assemblies usually have a lot of haplotypic duplications.
