Description Usage Arguments Details Author(s)
Main fastq quality function
1 2 | fastq_quality_control(inFile, illumninaclip, par_list, leading = 10,
trailing = 10, minlength = 50)
|
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 |
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
.
Jochen Kruppa
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