ggDNAvis : a ggplot2 -based R package for creating high-quality DNA sequence and modification visualisations

Abstract In the genomics age, enormous volumes of DNA sequencing information are continuously produced and analysed. Pipelines for processing DNA information are widespread and mature. However, tools for creating figure-ready visualisations of sequence and methylation information can be limited, often resulting in authors taking varied, manual approaches. ggDNAvis produces high-quality, extensively customisable renders of DNA sequences and modifications. The three core features are visualisation of a single sequence, multiple sequences, or methylation of multiple DNA molecules. Additionally, ggDNAvis has tools for reading/writing file formats such as FASTQ. Single-sequence visualisation accepts any DNA/RNA sequence from any source, so is extremely versatile and useful across biological contexts. Multiple-sequence visualisation was conceived in the context of visualising read-level long-read sequencing (e.g. Nanopore) daya to show intrasample variability in causative genes of repeat expansion diseases such as neuronal intranuclear inclusion disease (NIID) caused by NOTCH2NLC , Huntington’s disease (HD) caused by HTT , and fragile X syndrome (FXS) caused by FMR1 , but is applicable for visualising any set of multiple sequences. Methylation visualisation requires read-level methylation data, most commonly obtained via modification-capable basecalling of signal-level Nanopore data. ggDNAvis is available as a Shiny web app and a CRAN R package, with the latter supporting additional ggplot2 extension. Abstract Figure