Trimmomatic performs a variety of useful trimming tasks for illumina paired-end data.
java -jar <path to trimmomatic.jar> PE [-threads <threads] [-phred33 | -phred64] [-trimlog <logFile>] >] [-basein <inputBase> | <input 1> <input 2>] [-baseout <outputBase> | <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> ... or java -classpath <path to trimmomatic jar> org.usadellab.trimmomatic.TrimmomaticPE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] [-basein <inputBase> | <input 1> <input 2>] [-baseout <outputBase> | <paired output 1> <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> ...
Paired-end mode requires 2 input files (for forward and reverse reads) and 4 output files (for forward paired, forward unpaired, reverse paired and reverse unpaired reads).
fastaWithAdaptersEtc: specifies the path to a fasta file containing all the adapters, PCR sequences etc. The naming of the various sequences within this file determines how they are used. See the section below or use one of the provided adapter files.
seedMismatches: specifies the maximum mismatch count which will still allow a full match to be performed.
palindromeClipThreshold: specifies how accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment.
simpleClipThreshold: specifies how accurate the match between any adapter etc. sequence must be against a read.
minAdapterLength: In addition to the alignment score, palindrome mode can verify that a minimum length of adapter has been detected. If unspecified, this defaults to 8 bases, for historical reasons. However, since palindrome mode has a very low false positive rate, this can be safely reduced, even down to 1, to allow shorter adapter fragments to be removed.
keepBothReads: 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. For this reason, the default behaviour is to entirely drop the reverse read. By specifying „trueâ€Ÿ for this parameter, the reverse read will also be retained, which may be useful e.g. if the downstream tools cannot handle a combination of paired and unpaired reads.
windowSize: specifies the number of bases to average across.
requiredQuality: specifies the average quality required.
targetLength: This specifies the read length which is likely to allow the location of the read within the target sequence to be determined.
strictness: This value, which should be set between 0 and 1, specifies the balance between preserving as much read length as possible vs. removal of incorrect bases. A low value of this parameter (<0.2) favours longer reads, while a high value (>0.8) favours read correctness.
quality: Specifies the minimum quality required to keep a base.
length: The number of bases to keep, from the start of the read.