Visualization tools for human structural variations identified by whole-genome sequencing

Abstract

Visualizing structural variations (SVs) is a critical step for finding associations between SVs and human traits or diseases. Given that there are many sequencing platforms used for SV identification and given that how best to visualize SVs together with other data, such as read alignments and annotations, depends on research goals, there are dozens of SV visualization tools designed for different research goals and sequencing platforms. Here, we provide a comprehensive survey of over 30 SV visualization tools to help users choose which tools to use. This review targets users who wish to visualize a set of SVs identified from the massively parallel sequencing reads of an individual human genome. We first categorize the ways in which SV visualization tools display SVs into ten major categories, which we denote as view modules. View modules allow readers to understand the features of each SV visualization tool quickly. Next, we introduce the features of individual SV visualization tools from several aspects, including whether SV views are integrated with annotations, whether long-read alignment is displayed, whether underlying data structures are graph-based, the type of SVs shown, whether auditing is possible, whether bird's eye view is available, sequencing platforms, and the number of samples. We hope that this review will serve as a guide for readers on the currently available SV visualization tools and lead to the development of new SV visualization tools in the near future.

Opportunities and challenges in long-read sequencing data analysis

“…Therefore, validation of new variants has to be performed via other methods. Developing robust benchmarks is an ongoing effort [82], as is devising solutions to visualise complex, phased variants for critical assessment [82,83].…”

Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments

“…For example, we found no mention of effectiveness or usability assessment processes in articles about individual software tools, such as Tablet (a next-generation sequencing data viewer) [ 44 ], Artemis (a high-throughput sequencing visualisation tool) [ 45 ], and Aliview (an MSA browser) [ 46 ]. We find the same absence in review papers, such as a 2010 review of visualisation of MSAs, phylogenies, and gene family evolution [ 9 ], a 2020 review of visualisation tools for human structural variations [ 47 ], and many reviews of genome browsers [ 48 – 50 ]. Particularly now there are a large number of visualisation packages for MSAs and many other kinds of biological data, we recommend such assessments.…”

JBrowse 2: A modular genome browser with views of synteny and structural variation

“…Compared to other tools for visualizing structural variants and synteny, JBrowse 2 is most similar to general-purpose genome browsers (GBrowse-Syn and Artemis) in that it renders syntenic relationships between generic linear visualizations of genomes, their annotations, and supporting evidence. However, JBrowse 2 also includes views that draw extensively on user interface concepts pioneered by Ribbon and Circos, and indeed includes many of the views described in (Yokoyama and Kasahara 2020). These are all tied together by a modern web application framework that enables researchers to navigate between these different views, combining multiple coarse-grained, fine-grained, and non-linear views of the genome.…”

“…General purpose genome browsers such as IGV also remain popular for analyzing SVs (Robinson et al 2017). An overview of the various visual paradigms of structural variation can be found in (Yokoyama and Kasahara 2020).…”