New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads

Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. We present new algorithms for assembling long DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers se-lected by a hash function derived from the k-mer distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function. For diploid samples, we integrated a reim-plementation of the ReFHap algorithm to perform molecular phasing. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from haploid and diploid samples of different species. Our algorithms showed competitive accuracy and computational efficiency, compared with other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.

Automated summary

Building de novo genome assemblies for complex genomes is possible with long-read DNA sequencing technologies. New algorithms are developed to assemble long DNA sequencing reads from haploid and diploid organisms. The algorithms demonstrate competitive accuracy and computational efficiency compared with other software currently used. This development is expected to be useful for researchers building genome assemblies for different species.