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 | Defaultvalue |
---|---|---|
Input data | Set the type of the input reads: single-end (SE) or paired-end (PE). | 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):
| False |
Number of threads | Use multiple threads (-threads). | 8 |
To configure trimming steps use the following button:
<center> <br> <img src="/wiki/download/attachments/22059547/Improve Reads with Trimmomatic Element_0.png"/> <br> </center> |
The following dialog will appear:
<center> <br> <img src="/wiki/download/attachments/22059547/Improve Reads with Trimmomatic Element.png"/> <br> </center> |
Click the Add new step button and select a step. The following options are available:
Each step has the own parameters:
AVGQUAL
This step drops a read if the average quality is below the specified level.
Input the following values:
CROP
This step removes bases regardless of quality from the end of thread, so that the readhas maximally the specified length after this step has been performed. Steps performed after CROP might of course further shorten the read.
Input the following values:
HEADCROP
This step removes the specified number of bases, regardless of quality, from the beginning of the read.
Input the following values:
ILLUMINACLIP
This step is used to find and remove Illumina adapters.
Trimmomatic first compares short sections of an adapter and a read. If they match enough, the entire alignment between the read and adapter is scored. For paired-end reads, the "palindrome" approach is also used to improve the result. See Trimmomatic manual for details.
Input the following values:
There are also two optional parameters for palindrome mode: Min adapter length and Keep both reads. Use the following dialog. To call the dialog press the Optional button.
<center> <br> <img src="/wiki/download/attachments/22059547/Improve Reads with Trimmomatic Element_1.jpg"/> <br> </center> |
LEADING
This step removes low-quality bases from the beginning. As long as a base has a value below this threshold the base is removed and the next base will be investigated.
Input the following values:
MAXINFO
This step performs an adaptive quality trim, balancing the benefits of retaining longer reads against the costs of retaining bases with errors. See Trimmomatic manual for details.
Input the following values:
MINLEN
This step removes reads that fall below the specified minimum length. If required, it should normally be after all other processing steps. Reads removed by this step will be counted and included in the "dropped reads" count.
Input the following values:
SLIDINGWINDOW
This step performs a sliding window trimming, cutting once the average quality within the window falls below a threshold. By considering multiple bases, a single poor quality base will not cause the removal of high-quality data later in the read.
Input the following values:
TOPHRED33
This step (re)encodes the quality part of the FASTQ file to base 33.
TOPHRED64
This step (re)encodes the quality part of the FASTQ file to base 64.
TRAILING
This step removes low-quality bases from the end. As long as a base has a value below this threshold the base is removed and the next base (i.e. the preceding one) will be investigated. This approach can be used removing the special Illumina " low-quality segment" regions (which are marked with a quality score of 2), but SLIDINGWINDOW or MAXINFO are recommended instead.
Input the following values:
To remove a step use the Remove selected step button. The pink highlighting means the required parameter has not been set.
Type: trimmomatic
Parameter | Parameter in the GUI | Type |
---|---|---|
input-data | Input data | string |
trimming-steps | Trimming steps | string |
output-url | Output file | string |
generate-log | Generate detailed log | bool |
threads | Number of threads | numeric |
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 In GUI | Slot in Workflow File | Type |
---|---|---|
Output FASTQ URL | reads-url1 | string |