The workflow scans each input sequence from the end to find the first position where the quality is greater than or equal to the minimum quality threshold. Then it trims the sequence to that position. If the entire sequence has a quality lower than the threshold or if the length of the output sequence is less than the minimum length threshold, then the sequence is skipped.
Element type:QualityTrim
Parameters
Parameter
Description
Default Value
Parameter in Workflow File
Type
Output directory
Select an output directory. Custom – specify the output directory in the ‘Custom directory’ parameter. Workflow – internal workflow directory. Input file – the directory of the input file.
Input file
out-mode
numeric
Custom directory
Specify the output directory.
(not set)
custom-dir
string
Output file name
The name of an output file. If empty, the name of the first file will be used with an additional extension.
(not set)
out-name
string
Quality threshold
Quality threshold for trimming.
30
qual-id
numeric
Min Length
Too short reads are discarded by the filter.
0
len-id
numeric
Trim both ends
Trim both ends of a read. Usually set to True for Sanger sequencing and False for NGS.