The current trimming steps are:
ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read. SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold.
LEADING: Cut bases off the start of a read, if below a threshold quality
TRAILING: Cut bases off the end of a read, if below a threshold quality
CROP: Cut the read to a specified length
HEADCROP: Cut the specified number of bases from the start of the read
MINLEN: Drop the read if it is below a specified length
TOPHRED33: Convert quality scores to Phred-33
TOPHRED64: Convert quality scores to Phred-64
It works with FASTQ (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp'ed FASTQ. Use of gzip format is determined based on the .gz extension.
For single-ended data, one input and one output file are specified, plus the processing steps. For paired-end data, two input files are specified, and 4 output files, 2 for the 'paired' output where both reads survived the processing, and 2 for corresponding 'unpaired' output where a read survived, but the partner read did not.
Trimmomatic is a java program accessed via a modules library on the lab cluster.
module load trimmomatic
This loads the default version of Trimmomatic and sets the environment variable TRIMMOMATIC.
Then invoke the program:
java -jar $TRIMMOMATIC/trimmomatic.jar
java -Xmx2000M -jar $TRIMMOMATIC/trimmomatic.jar PE R1.fastq R2.fastq R1.PE.fastq R1.SE.fastq R2.PE.fastq R2.SE.fastq ILLUMINACLIP:$TRIMMOMATIC/adapters/NexteraPE-PE.fa:2:30:10:2:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30
The user manual is available at http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
Consider using the risstrim.pl script in the riss_util module, which provides a simplified interface for running Trimmomatic.
module load riss_util