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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)
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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.

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

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.

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


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