denoise_file {debar}

Denoise sequence data from a given file.

Description

This function allows for direct input to output exectution of the denoising pipeline. All paramaters for the fasta/fastq input and output functions as well as the denoise pipeline can be passed to this function. Please consult the documentation for those functions for a list of available paramaters. The function will run the denoise pipeline with the specified paramaters for all sequences in the input file, and write the denoised sequences and corresponding header/quality information to the output file. Additionally the function allows for rejected reads to be kept and sequestered to an additional output file (as opposed to being discarded) and also allows for a log file to be produced that tracks several statistics including the execition time, number of denoised reads and number of rejected reads.

Usage

denoise_file(x, ...)

## Default S3 method:
denoise_file(x, ..., outfile = "output.fastq",
  informat = "fastq", outformat = "fastq", to_file = TRUE,
  log_file = FALSE, keep_rejects = FALSE, multicore = FALSE)

Arguments

x

The name of the file to denoise sequences from.

...

additional arguments to be passed to the denoise and input/output functions.

outfile

The name of the file to output sequences to.

informat

The format of the file to be denoised. Options are fastq or fasta. Default is fastq.

outformat

The format of the output file. Options are fasta or fastq (default) format.

to_file

Boolean indicating whether the sequence should be written to a file. Default is TRUE.

log_file

Boolean indicating if a log file should be produced. Default is FALSE.

keep_rejects

Boolean indicating if the bad reads should be written to a separate file (with the name "rejects_" + outfile). Defaut is FALSE.

multicore

An integer specifying the number of cores over which to multithread the denoising process. Default is FALSE, meaning the process is not multithreaded.

Details

Using this function is optimized by the appropriation of the multicore option, which allows a user to specify a number of cores that the denoising process should be multithreaded across. The more cores available, the faster the denoising of the input data. It should be noted that the multithreading relies on the entire fastq file being read into memory, because of this your machine's available ram will need to exceed the size of the unzipped fastq file being denoised. If your file size exceeds the available memory you may want to consider spliting the input into several smaller files and denoising them each with this function (this is a fast solution as the multicore option can be used to speed up denoising). Alternatively, you can depoly the 'denoise' function in an iterative fashion, reading in/denoising and writing only a single fq entry at a time. This would require a much smaller memory footprint, but would be much slower due to the lack of multithreading.

See Also

denoise