assembly-stats | Assembly statistic visualisation

assembly-stats is a JavaScript library. assembly-stats has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

A de novo genome assembly can be summarised by a number of metrics, including:. assembly-stats supports two widely used presentations of these values, tabular and cumulative length plots, and introduces an additional circular plot that summarises most commonly used assembly metrics in a single visualisation. Each of these presentations is generated using javascript from a common (JSON) data structure, allowing toggling between alternative views, and each can be applied to a single or multiple assemblies to allow direct comparison of alternate assemblies. Tabular presentation allows direct comparison of exact values between assemblies, the limitations of this approach lie in the necessary omission of distributions and the challenge of interpreting ratios of values that may vary by several orders of magnitude. Cumulative scaffold length plots are highly effective for comparison of two or more assemblies, plotting both on a single set of axes reveals differences in assembled size and the N50 count very clearly. However, other metrics must still be tabulated or annotated on the plot for example N50 length and the longest scaffold length can be particularly difficult to determine from the plot alone. The scale for the axes is usually chosen to accommodate the data for a single assembly or set of assemblies, meaning that it is usually necessary to replot the data or consider the relative axis scales carefully to compare assemblies that have been plotted separately. The cumulative distribution plots in assembly-stats address the problem of scaling by allowing any combination of assemblies to be plotted together and allowing rescaling of the axes to fit any one of the individual assemblies. The circular plots have been introduced to overcome some of the shortcomings of tabular and cumulative distribution plots in a visualisation that allows rapid assessment of most common assembly metrics. The graphic is essentially scale independent so assemblies of any size with different strengths and weaknesses produce distinct patterns that can be recognised at a glance. While side by side presentation of a pair of assemblies on consistently scaled axes allows direct comparison, the standard presentation is designed to facilitate assessment of overall assembly quality by consideration of the keys features from the plot.