A Comparative Study of HiCanu and Hifiasm

Abstract

The recent development of Hifi sequencing has greatly improved people's understanding of genomics. Hifi reads provide a more accurate and complete picture than traditional long reads and Illumina short reads. However, both long reads and short reads assemblers are not good fits for Hifi reads in reality. Therefore, in late 2020, HiCanu and Hifiasm have been developed to assemble Hifi reads. Even though they are both phased assemblers, which highly complexed regions will be separated into two different alleles, they show different output formats, algorithms and performance. The topic of this paper will be focused on comparison between HiCanu and Hifiasm on contiguity, completeness, and runtime. In order to compare the two tools, it is necessary to examine HiCanu and Hifiasm results of different genome assemblies from several published papers. Despite some shortcomings of Hifiasm assembler which is associated with increased coverage, Hifiasm is the best assembler for Hifi reads so far because of its high contiguity, completeness and fast runtime.