An R package for producing sequence similarity dotplots. Uses a sparse matrix representation and parallelism to reduce memory usage and speed up computations. This package also handles reverse complement matches and outputs a customisable ggplot object. This has been tested with sequences up to 150kb long.
You can install the development version of seqdotplot from GitHub with:
if (!require("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("shians/seqdotplot")library(seqdotplot)
seq <- readLines(system.file(package = "seqdotplot", "dxz4_cast_ref.fa"))[2]
sub_seq <- substr(seq, 68000, 74000)
seqdotplot(sub_seq, sub_seq, threads = 2)