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IONiseR (version 1.2.2)

Quality Assessment Tools for Oxford Nanopore MinION data

Description

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

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Version

Version

1.2.2

License

MIT + file LICENSE

Maintainer

Mike Smith

Last Published

February 15th, 2017

Functions in IONiseR (1.2.2)

baseCalled

Extract baseCalled slot
channelActivityPlot

Visualise a specified metric over all channels over time.
muxHeatmap

Create layout plot of flowcell
plotActiveChannels

Plot the number of active channels for each minute of run time
rawData

Extract rawData slot
readFast5Summary

Read summary data from fast5 files.
IONiseR

IONiseR: A package for assessing quality of MinION data
layoutPlot

Create layout plot of flowcell
plotReadAccumulation

Plot the accumulation of reads over the duration of the experiment.
plotReadCategoryCounts

Plot the proportion of template, complement and 2D reads found a dataset.
readInfo

Extract readInfo slot
fastq

Extract fastq slot
fastq2D

Extract 2D reads
plotEventRate

Plot the mean rate at which events occur
plotKmerFrequencyCorrelation

Display correlation between pentemer proportions in two time windows
readInfo,Fast5Summary-method

An S4 class for summarised data from a MinION sequencing run
channelHeatmap

Create layout plot of flowcell
plotBaseProductionRate

Plot the mean rate at which bases are recorded
plotCurrentByTime

View changes in signal against run time.
fastqComplement

Extract complement reads
fastqTemplate

Extract template reads
plotReadCategoryQuals

Visualise the mean base quality of each read
plotReadTypeProduction

View changes in signal against run time.