I'm trying to assemble the de novo genome of a triploid eukaryote, w/ genome size of ca. 3.2Gbp. I've got ~50x coverage of PacBio HiFi, and also 50x of Illumina HiSeq 150x150. The HiFi assembly is obviously quite redundant, with nearly all BUSCOs found in triplicate. This isn't entirely surprising -- but I haven't been able to find a way to merge these contigs into a single haploid assembly yet that doesn't require a reference. I'm not worried about phasing or reconstructing contiguous haplotypes, but rather simply a (collapsed?) representative assembly that isn't inflated by 300%. Existing tools still seem geared to unzipping diploid assemblies.
Any help appreciated!
Any help appreciated!