Shians / PorexploreR

Bob Loblaw's Law Blog Applauds Porexplorer

PorexploreR

PorexploreR is a package for exploring raw Nanopore sequencing signals.

Installation

You can install the released version of PorexploreR from GitHub with:

if (!require(remotes)) install.packaages("remotes")
remotes::install_github("shians/PorexploreR")

Example

library(PorexploreR)

# get example file from package
fast5_file <- system.file("extdata/NA12878_short_read2.fast5", package = "PorexploreR")

# load in the squiggle
squiggle <- Squiggle(fast5_file)

# plot the squiggle
plot_squiggle(squiggle)

# some other information obtainable
raw_signal(squiggle)  # signal as stored in fast5 file
signal(squiggle)      # signal transformed to pA scale
meta(squiggle)        # metadata used to transform signal

See Also

R Packages

• NanoR - A user-friendly R package to analyze and compare nanopore sequencing data.
• poRe - An R package to enable visualisation of nanopore sequencing data.
• IONiseR - Quality assessment tools for Oxford Nanopore MinION data.

Further Reading

• A Look at the Nanopore fast5 Format - My blog article on exploring the fast5 format.