AlleleProfileR.qc: QC reads using external software

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

Description

QC reads using external software. Currently only fastp is available. This external software needs to be installed manually and needs to be addressable from the terminal.

Usage

AlleleProfileR.qc(files, method = "fastp", params = "",
  subset = NULL)

Arguments

files	Vector with files. Output of AlleleProfileR.read.folders
method	QC method. Default is fastp.
params	String with additional parameters
subset	Vector with the indices of the entries that should be processed. Default is NULL, all entries will be analyzed.

Author(s)

Arne Bruyneel

References

• Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560

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