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  • FASTQ Quality Trimmer Element
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The workflow scans each input sequence from the end to find the first position where the quality is greater or equal to the minimum quality threshold. Then it trims the sequence to that position. If a the whole sequence has quality less than the threshold or the length of the output sequence less than the minimum length threshold then the sequence is skipped.

Parameters in GUI

ParameterDescriptionDefault value
Output directorySelect 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
Custom directory

Specify the output directory.

Output file nameA name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. 
Quality thresholdQuality threshold for trimming.30
Min LengthToo short reads are discarded by the filter.0
Trim both endsTrim the both ends of a read or not. Usually, you need to set True for Sanger sequencing and False for NGSTrue

Parameters in Workflow File 

Type: QualityTrim

ParameterParameter in the GUIType
out-modeOutput directorynumeric
custom-dirCustom directorystring
out-nameOutput file namestring
qual-idQuality thresholdnumeric
len-idMin Lengthnumeric
both-endsTrim both endsboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Input File

Name in Workflow File: in-file


Slot In GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: Output File

Name in Workflow File: out-file


Slot In GUISlot in Workflow FileType
Source URLurlstring
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