AlleleProfileR.preprocess: Preprocess fastq.gz files

In abruyneel/AlleleProfileR: Genome editing strategy agnostic variant identification and profiling tool

Description

This function executes QC (fastp), merges paired reads (pear), and maps the reads to the reference (BWA). This external software needs to be installed manually and needs to be addressable from the terminal.

Usage

AlleleProfileR.preprocess(files, index, method.qc = "fastp",
  params.qc = "", method.merge = "pear", params.merge = "-v 10",
  method.map = "bwa", subset = NULL)

Arguments

files	Vector with files. Output of AlleleProfileR.read.folders
index	Path to the .fa file containing the reference genome.
method.qc	Method for conducting QC on raw reads. Currently only fastp is implemented. Use 'none' to skip this step.
params.qc	Additional parameters for conducting QC on raw reads.
method.merge	Method for merging paired reads. Currently only pear and fastq-join are implemented.
params.merge	Additional parameters for merging paired reads
method.map	Method for mapping reads to reference. Currently only BWA is implemented.
subset	Vector with the indices of the entries that should be processed. Default is NULL, all entries will be analyzed.

Author(s)

Arne Bruyneel

abruyneel/AlleleProfileR documentation built on June 12, 2020, 2:47 p.m.