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Removes adapter sequences.

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
Output file name

A 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.

 
FASTA file with 3' adaptersA FASTA file with one or multiple sequences of adapter that were ligated to the 3' end. The adapter itself and anything that follows is trimmed. If the adapter sequence ends with the '$ character, the adapter is anchored to the end of the read and only found if it is a suffix of the read. 
FASTA file with 5' adaptersA FASTA file with one or multiple sequences of adapters that were ligated to the 5' end. If the adapter sequence starts with the character '^', the adapter is 'anchored'. An anchored adapter must appear in its entirety at the 5' end of the read (it is a prefix of the read). A non-anchored adapter may appear partially at the 5' end, or it may occur within the read. If it is found within a read, the sequence preceding the adapter is also trimmed. In all cases, the adapter itself is trimmed. 
FASTA file with 5' and 3' adaptersA FASTA file with one or multiple sequences of adapters that were ligated to the 5' end or 3' end. 

Parameters in Workflow File 

Type: CutAdaptFastq

ParameterParameter in the GUIType
out-modeOutput directorystring
out-nameOutput file namestring
adapters-urlFASTA file with 3' adaptersstring
front-urlFASTA file with 5' adaptersstring
anywhere-urlFASTA file with 5' and 3' adaptersstring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input File

Name in Workflow File: in-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: Output File

Name in Workflow File: out-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring
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