ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization

Garrido Martín, Diego, 1992-; Palumbo, Emilio; Guigó Serra, Roderic; Breschi, Alessandra, 1988-

doi:http://dx.doi.org/10.1371/journal.pcbi.1006360

ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization

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Citation

Garrido-Martín D, Palumbo E, Guigó R, Breschi A. ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization. PLoS Comput Biol. 2018;14(8):e1006360. DOI: 10.1371/journal.pcbi.1006360

Abstract

We present ggsashimi, a command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments, a feature unique to this software. Compared to the existing versions of programs generating sashimi plots, it uses popular bioinformatics file formats, it is annotation-independent, and allows the visualization of splicing events even for large genomic regions by scaling down the genomic segments between splice sites. ggsashimi is freely available at https://github.com/guigolab/ggsashimi. It is implemented in python, and internally generates R code for plotting.