Improve Reads with Trimmomatic Element

Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters.

Parameters in GUI

Parameter	Description	Default value
Input data	Set the type of the input reads: single-end (SE) or paired-end (PE). One or two slots of the input port are used depending on the value of the parameter. Pass URL(s) to data to these slots. Note that the paired-end mode will use additional information contained in paired reads to better find adapter or PCR primer fragments introduced by the library preparation process.	SE reads
Trimming steps	Configure trimming steps that should be performed by Trimmomatic.	configure steps
Output file	Specify the output file name.	auto
Generate detailed log	Select "True" to generate a file with log of all read trimmings, indicating the following details (-trimlog): the read name the surviving sequence length the location of the first surviving base, aka. the amount trimmed from the start the location of the last surviving base in the original read the amount trimmed from the end	False
Number of threads	Use multiple threads (-threads).	8

To configure trimming steps use the following button:

Parameters in Workflow File

Type: trimmomatic

The element has 1 input port:

Name in GUI: Input FASTQ file(s)

Name in Workflow File: in

Slots:

Slot In GUI	Slot in Workflow File	Type
Input FASTQ URL	reads-url1	string

And 1 output port:

Name in GUI: Improved FASTQ file(s)

Name in Workflow File: out-file

Slots:

Slot InGUI	Slot in Workflow File	Type
Output FASTQ URL	reads-url1	string