Trimmomatic

Description

trimmomatic website

Trimmomatic performs a variety of useful trimming tasks for Illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. 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.

Environment Modules

Run module spider trimmomatic to find out what environment modules are available for this application.

Environment Variables

• HPC_TRIMMOMATIC_DIR - installation directory
• HPC_TRIMMOMATIC_ADAPTER - adapter file directory

Categories

biology, ngs