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Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the  de novo  assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided  de novo  assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences (PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms.

Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data