Trimmomatic
Description
!! Under Development !!
From the Trimmomatic Home Page: 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.
Version
- 0.36
Authorized Users
- CIRCE account holders
- SC account holders
Platforms
CIRCEclusterRRAclusterSCcluster
Modules
- apps/trimmomatic/0.36
Running Trimmomatic on CIRCE/SC
The Trimmomatic user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.
- Note on CIRCE: Make sure to run your jobs from your $WORK directory!
- Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
Batch Job submission
To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 30 minutes to run on a standard PC.
#!/bin/bash #SBATCH --job-name=test_trimmomatic #SBATCH --time=04:00:00 #SBATCH -N 1 #SBATCH --ntasks-per-node=4 #SBATCH --mem-per-cpu=2096 #SBATCH -o output.%j.%N.txt #SBATCH -e error.%j.%N.txt #### SLURM single node trimmomatic test #### to run for 4 hours #### using 4 processing cores and 8GB of memory # Unload all modules, then load the trimmomatic module: module purge module load apps/trimmomatic #always run in WORK when running batch jobs mkdir $WORK/trim_ex cp $HOME/trim_ex/*fastq $WORK/trim_ex cd $WORK/trim_ex #computation steps java -jar /apps/trimmomatic/0.36/bin/trimmomatic.jar PE -threads 4 -phred33 SRR6202537_1.fastq SRR6202537_1.fastq SRR6202537_out_forward_paired.fastq SRR6202537_out_forward_unpaired.fastq SRR6202537_out_reverse_paired.fastq SRR6202537_out_reverse_unpaired.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 cp *.fastq $HOME/trim_ex
Next, you can change to your job’s directory, and run the sbatch command to submit the job:
[user@login0 ~]$ cd my/jobdir [user@login0 jobdir]$ sbatch ./test_subread.sh
- You can view the status of your job with the “squeue -u <username>” command
Documentation
Home Page, User Guides, and Manuals
- Trimmomatic Home Page:
- Trimmomatic User Guide:
Benchmarks, Known Tests, Examples, Tutorials, and Other Resources
- Trimmomatic Examples
- /apps/trimmomatic/0.36/examples
More Job Information
See the following for more detailed job submission information:
Reporting Bugs
Report bugs with Trimmomatic to the IT Help Desk: rc-help@usf.edu