HyPo: Super fast and accurate polisher for long read genome assemblies

Efforts towards making population-scale long read genome assemblies (especially human genomes) viable have intensified recently with the emergence of many fast assemblers. The reliance of these fast assemblers on polishing for the accuracy of assemblies makes it crucial.

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).

The tool and its source code are available on GitHub: https://github.com/kensung-lab/hypo.