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While many short read assemblers attempt to simplify the de Brujin graph byidentifying and resolving variant-induced bubbles to produce a haploid mosaicresult, this approach is only viable when variants are relatively rare and thebubbles are well defined in a graph context. We observed that diploid genomeswith very high levels of heterozygosity fail to display well-resolved bubblestructures in a typical assembly graph and thus result in highly fragmented andincomplete assemblies. Here we present an enhancement of Meraculous2 algorithm,called Meraculous-2D, which preserves haplotypes across variant sites andgenerates accurate assembly of highly heterozygous diploid genomes. Preservingand taking advantage of the allelic variation throughout the assembly processallows reconstructing both haplomes at once, without the need to pick arbitrarypaths through bubble structures. We also enhanced the original diploidyresolution method of Meraculous2 to maintain and report phased haplotypevariant information.

Meraculous-2D: Haplotype-sensitive Assembly of Highly Heterozygous genomes