fastq_quality_control: Main fastq quality function

In jkruppa/virDisco: Modules for a viral detection pipeline

Description

Main fastq quality function

Usage

fastq_quality_control(inFile, illumninaclip, par_list, leading = 10,
  trailing = 10, minlength = 50)

Arguments

inFile	Fastq infile
illumninaclip	Remove the adapter from illumina by TruSeq2 or TruSeq3 protocol
par_list
leading	Numeric. Remove leading low quality or N bases (below quality 10 [default])
trailing	Numeric. Remove trailing low quality or N bases (below quality 10 [default])
minlength	Min read length to keep. 50 [default]
log_file	write the trimmomatic output to file

Details

Main fastq quality function. Calls the function fastq_trimmer [internal]. Stores files in a tempDir. The external function trimmomatic is needed and the file path has to be stored in the program_list, see set_program_list.

Author(s)

Jochen Kruppa

jkruppa/virDisco documentation built on May 3, 2019, 7:05 p.m.