Abstract
BackgroundAccurate de novo genome assembly has become reality with the advancements in sequencing technology. With the ever-increasing number of de novo genome assembly tools, assessing the quality of assemblies has become of great importance in genome research. Although many quality metrics have been proposed and software tools for calculating those metrics have been developed, the existing tools do not produce a unified measure to reflect the overall quality of an assembly.ResultsTo address this issue, we developed the de novo Assembly Quality Evaluation Tool (dnAQET) that generates a unified metric for benchmarking the quality assessment of assemblies. Our framework first calculates individual quality scores for the scaffolds/contigs of an assembly by aligning them to a reference genome. Next, it computes a quality score for the assembly using its overall reference genome coverage, the quality score distribution of its scaffolds and the redundancy identified in it. Using synthetic assemblies randomly generated from the latest human genome build, various builds of the reference genomes for five organisms and six de novo assemblies for sample NA24385, we tested dnAQET to assess its capability for benchmarking quality evaluation of genome assemblies. For synthetic data, our quality score increased with decreasing number of misassemblies and redundancy and increasing average contig length and coverage, as expected. For genome builds, dnAQET quality score calculated for a more recent reference genome was better than the score for an older version. To compare with some of the most frequently used measures, 13 other quality measures were calculated. The quality score from dnAQET was found to be better than all other measures in terms of consistency with the known quality of the reference genomes, indicating that dnAQET is reliable for benchmarking quality assessment of de novo genome assemblies.ConclusionsThe dnAQET is a scalable framework designed to evaluate a de novo genome assembly based on the aggregated quality of its scaffolds (or contigs). Our results demonstrated that dnAQET quality score is reliable for benchmarking quality assessment of genome assemblies. The dnQAET can help researchers to identify the most suitable assembly tools and to select high quality assemblies generated.
Highlights
Accurate de novo genome assembly has become reality with the advancements in sequencing technology
We showed that the well-established metrics could present contradictory results to each other using six de novo assemblies for sample NA24385 and our quality score was effective to unify these metrics into a single score to reflect their overall quality
We proposed a framework to compute quality measures based on a trusted reference genome to evaluate (i) quality of the scaffolds of a de novo assembly and (ii) the overall quality of a de novo assembly based on the individual qualities of its scaffolds
Summary
Accurate de novo genome assembly has become reality with the advancements in sequencing technology. As sequencing has become cheaper and more affordable, the challenge of routinely applying NGS in the precision medicine era largely rests on bioinformatics solutions, especially for personal genome assembly in near future. For this purpose, various assembly tools have been proposed and reported in the literature for de novo assembly using short-read and long-read NGS data. In another study [19], the authors compared de novo assemblies generated by multiple assembly tools for human chromosome 14 and three other organisms with small genomes These works established the groundwork for some of the well-accepted metrics to measure the quality of an assembly from multiple perspectives
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