Evaluation of combined genome assemblies: A case study with fungal genomes

Abstract

The rapid advances in genome sequencing leads to the generation of huge amount of data in a single sequencing experiment. Several genome assemblers with different objectives were developed to process these genomic data. Obviously, the output assemblies produced by these assemblers have different qualities due to their diverse nature. Recent research efforts concluded that combining the assemblies from different assemblers would enhance the quality of the output assembly. Based on this, our study combines the five best assemblies of three fungal genomes and evaluates the quality of the output assembly as compared to that produced by individual assemblers. The results conclude that the output assembly quality is influenced by the increase of the number of gaps in the input assemblies more than the increase in N50 size. Based on this conclusion, we propose a set of guidelines to get better output assemblies.