fast5toFastq: Extract FASTQ files from fast5 files

In grimbough/IONiseR: Quality Assessment Tools for Oxford Nanopore MinION data

Description

This function provides direct access to the FASTQ entries held within fast5 files. If you are only interested in getting hold of the base called reads, and don't require any raw-signal or event information, use this function. Given a vector of fast5 files, the FASTQ entries will be combined and up to three gzip compressed FASTQ will be created - one for each of the template, complement and 2D strands depending upon what is available in the input files.

Usage

fast5toFastq(files, strand = "all", fileName = NULL, outputDir = NULL,
  ncores = 1)

Arguments

files	Character vector of fast5 files to be read.
strand	Character vector specifying the strand to extract. Can take any combination of the following options: "template", "complement", "2D", "all", "both".
fileName	Stem for the name of the names of the output file names. The appropriate strand will be appended to each file e.g. fileName_complement.fq.gz or fileName_template.fq.gz
outputDir	Directory output files should be written to.
ncores	Specify the number of CPU cores that should be used to process the files. Currently this seems to be more IO bound than CPU, so there is little benefit achieved by using a high number of cores.

Value

No value returned. Run for the side effect of writing the FASTQ files to disk.

Examples

## Not run: 
fast5files <- list.files('/foo/bar/', pattern = '.fast5$')
summaryData <- readFast5Summary(fast5files)

## End(Not run)

grimbough/IONiseR documentation built on Sept. 24, 2020, 11:32 a.m.