We present HyPo–a Hybrid Polisher–that utilises short as well as long reads within a single run to polish a long read assembly of small and large genomes. It exploits unique genomic kmers to selectively polish segments of contigs using partial order alignment of selective read-segments. As demonstrated on human genome assemblies, Hypo generates significantly more accurate polished assemblies in about one-third time with about half the memory requirements in comparison to Racon (the widely used polisher currently).
https://www.biorxiv.org/content/10.1101/2019.12.19.882506v1.abstract