Snail plots are badges of genome assembly quality

Abstract

Assembly quality is frequently assessed using independent measures of assembly span, contiguity, sequence composition and completeness. Among contiguity metrics, contig and scaffold N50 have perhaps gained the most traction, despite well known limitations. Several authors have suggested considering the complete Nx curve rather than just the N50 value, but while using N90 values or considering the area under the Nx curve with auN statistics provide more complete measures of contiguity, they share the limitation of being unsuited to direct comparison across a range of genome sizes. We introduced snail plots to provide a genome-size independent way to summarise a range of commonly used assembly metrics. Here we demonstrate that easily-learnt visual differences between snail plots allow simultaneous consideration of metrics across several key areas of assembly quality to rapidly identify high- and low-quality assemblies. We show that prominent features in snail plots of high-quality assemblies effectively highlight N50, N90 and auN contiguity statistics, but since the presentation is scaled to the longest scaffold, plots can be compared effectively across a wide range of taxa and assembly sizes. We use the core features of a snail plot to derive a proportional measure of assembly quality based on auN, adjusted for ambiguous, N, bases and scaled to the length of the longest scaffold. We show that this "snail score" value corresponds closely to a qualitative assessment of overall assembly quality from visual interpretation of a snail plot.