Component: Trimmomatic

Trimmomatic

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.

Adaptor removal is performed first if adapters are provied. After that the trimming operations, as defined by the parameters, are performed in the following order: leading, trailing, slidingWindow, headcrop, crop and minlen.

Version	2.1
Bundle	sequencing
Categories	Quality control
Authors	Ping Chen (ping.chen@helsinki.fi), Javier Nunez Fontarnau (javier.nunez-fontarnau@helsinki.fi), Alejandra Cervera (alejandra.cervera@helsinki.fi), Erkka Valo (erkka.valo@helsinki.fi)
Issue tracker	View/Report issues
Requires	trimmomatic-0.32.jar (jar) ; installer (bash)
Source files	component.xml TrimmomaticComponent.java
Usage	Example with default values Trimmomatic( read = FASTQ, //mate = FASTQ, //adapter = FASTA, crop = -1, gzip = false, headcrop = -1, illuminaAdapter = "", keepBothReads = false, leading = 30, minlen = 30, palindromeClip = 30, qual = "phred64", seedMM = 2, simpleClip = 12, slidingWindow = "null", threads = 4, trailing = 30 )

Version

2.1

Bundle

sequencing

Categories

Quality control

Authors

Ping Chen (ping.chen@helsinki.fi), Javier Nunez Fontarnau (javier.nunez-fontarnau@helsinki.fi), Alejandra Cervera (alejandra.cervera@helsinki.fi), Erkka Valo (erkka.valo@helsinki.fi)

Issue tracker

View/Report issues

Requires

trimmomatic-0.32.jar (jar) ; installer (bash)

Source files

component.xml TrimmomaticComponent.java

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
read	FASTQ	Mandatory	Sequence files in FASTQ format.
mate	FASTQ	Optional	Sequence files in FASTQ format.
adapter	FASTA	Optional	Fasta file for adapters.

Name

Type

Mandatory

Description

read

FASTQ

Mandatory

Sequence files in FASTQ format.

mate

FASTQ

Optional

Sequence files in FASTQ format.

adapter

FASTA

Optional

Fasta file for adapters.

Outputs

Name	Type	Description
trimmedReads	Array<FASTQ>	An array with trimmed reads. The keys are 'Reads', 'Mates', and 'Uread' and 'Umate' for unpaired reads and mates.
stdout	BinaryFile	Stdout of Trimmomatic.
stats	CSV	Short statistics.
log	TextFile	Log

Name

Type

Description

trimmedReads

Array<FASTQ>

An array with trimmed reads. The keys are 'Reads', 'Mates', and 'Uread' and 'Umate' for unpaired reads and mates.

stdout

BinaryFile

Stdout of Trimmomatic.

stats

CSV

Short statistics.

log

TextFile

Log

Parameters

Name	Type	Default	Description
crop	int	-1	Cut the read so it has maximally the specified length. The number of bases to keep, from the start of the read. No trimming is done if the value is set to -1.
gzip	boolean	false	Defines if the output sequences should be gzipped or not.
headcrop	int	-1	The number of bases to remove from the start of the read. No trimming is done if the value is set to -1.
illuminaAdapter	string	""	Illumina-specific sequences from the read included with Trimmomatic. Choose TruSeq2-SE.fa, TruSeq2-PE.fa, TruSeq3-SE.fa, or TruSeq3-PE.fa for specifying the file to use; leave it blank otherwise.
keepBothReads	boolean	false	Defines if keep the reverse reads after read-though has been detected by palindrome mode, and the adapter sequence removed, the reverse read contains the same sequence information as the forward read, albeit in reverse complement.
leading	int	30	Remove bases from the start of the read, if quality value is below the given threshold. Specifies the minimum quality required to keep a base. No trimming is done if the value is set to -1.
minlen	int	30	Specifies the minimum length of reads to keep. Reads are dropped if they are below a specified length. No reads are dropped if the value is set to -1.
palindromeClip	int	30	Specifies how accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment.
qual	string	"phred64"	Quality scores. Either 'phred33' or 'phred64'.
seedMM	int	2	Seed mismatched for adapters. It specifies the maximum mismatch count which will still allow a full match to be performed.
simpleClip	int	12	A threshold specifies how accurate the match between any adapter etc. sequence must be against a read. Each matching base adds just over 0.6. Thus, a perfect match of a 20 base sequence will score just over 12, while 25 bases are needed to score 15.
slidingWindow	string	"null"	Sliding window trimming where the sequence is cut if the average quality of the bases within the sliding window falls below the defined threshold. A string specifies the window size and the average required quality in the sliding window. The format is windowSize:requiredQuality. For example, 4:15 (window size = 4; required quality = 15). No trimming is done if value is set to 'null'.
threads	int	4	The number of threads to use.
trailing	int	30	Remove bases from the end of the read, if quality value is below the given threshold. Specifies the minimum quality required to keep a base. No trimming is done if the value is set to -1.

Name

Type

Default

Description

crop

int

-1

Cut the read so it has maximally the specified length. The number of bases to keep, from the start of the read. No trimming is done if the value is set to -1.

gzip

boolean

false

Defines if the output sequences should be gzipped or not.

headcrop

int

-1

The number of bases to remove from the start of the read. No trimming is done if the value is set to -1.

illuminaAdapter

string

Illumina-specific sequences from the read included with Trimmomatic. Choose TruSeq2-SE.fa, TruSeq2-PE.fa, TruSeq3-SE.fa, or TruSeq3-PE.fa for specifying the file to use; leave it blank otherwise.

keepBothReads

boolean

false

Defines if keep the reverse reads after read-though has been detected by palindrome mode, and the adapter sequence removed, the reverse read contains the same sequence information as the forward read, albeit in reverse complement.

leading

int

Remove bases from the start of the read, if quality value is below the given threshold. Specifies the minimum quality required to keep a base. No trimming is done if the value is set to -1.

minlen

int

Specifies the minimum length of reads to keep. Reads are dropped if they are below a specified length. No reads are dropped if the value is set to -1.

palindromeClip

int

Specifies how accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment.

qual

string

"phred64"

Quality scores. Either 'phred33' or 'phred64'.

seedMM

int

Seed mismatched for adapters. It specifies the maximum mismatch count which will still allow a full match to be performed.

simpleClip

int

A threshold specifies how accurate the match between any adapter etc. sequence must be against a read. Each matching base adds just over 0.6. Thus, a perfect match of a 20 base sequence will score just over 12, while 25 bases are needed to score 15.

slidingWindow

string

"null"

Sliding window trimming where the sequence is cut if the average quality of the bases within the sliding window falls below the defined threshold. A string specifies the window size and the average required quality in the sliding window. The format is windowSize:requiredQuality. For example, 4:15 (window size = 4; required quality = 15). No trimming is done if value is set to 'null'.

threads

int

The number of threads to use.

trailing

int

Remove bases from the end of the read, if quality value is below the given threshold. Specifies the minimum quality required to keep a base. No trimming is done if the value is set to -1.

Test cases

Test case	Parameters▼	IN read	IN mate	IN adapter	OUT trimmedReads	OUT stdout	OUT stats	OUT log
case1	properties	read	mate	adapter	trimmedReads	(missing)	stats	(missing)
	qual=phred33
case2	properties	read	(missing)	(missing)	trimmedReads	(missing)	stats	(missing)
	headcrop=10, leading=-1, trailing=-1
case3	properties	read	(missing)	(missing)	trimmedReads	(missing)	stats	(missing)
	qual=phred33, slidingWindow=4:30
case4_no_trimming	properties	read	mate	(missing)	(missing)	stdout	stats	(missing)
	qual=phred33, leading=-1, minlen=-1, trailing=-1

Test case

Parameters▼

IN
read

IN
mate

IN
adapter

OUT
trimmedReads

OUT
stdout

OUT
stats

OUT
log

case1

properties

read