Cut Adapter Element

Removes adapter sequences.

Parameters in GUI

Parameter	Description	Default value
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
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' adapters	A 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' adapters	A 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' adapters	A 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

The element has 1 input port:

Name in GUI: Input File

Name in Workflow File: in-file

Slots:

Slot In GUI	Slot in Workflow File	Type
Source URL	url	string

And 1 output port:

Name in GUI: Output File

Name in Workflow File: out-file

Slots:

Slot In GUI	Slot in Workflow File	Type
Source URL	url	string