Trimmomatic
Trimmomatic is a tool for trimming Illumina FASTQ data and removing adapters. When data is sequenced on Illumina, adapters are added for the fragments to attach to the beads. If these adapters are not removed they can result in false assembly or other issues. Additionally, the quality of the sequences varies across the length of the read, and poorer quality regions can be trimmed using Trimmomatic. Running Trimmomatic is a good first step in quality filtering your Illumina data.
To run it on the HPCC (for example trimming paired-end reads):
1 | |
Read the manual for how to use it.
If you prefer to load the Trimmomatic module using module load Trimmomatic, you can use the environment variable $EBROOTTRIMMOMATIC as a shorthand for the path above. Trimmomatic can then be executed using java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.39.jar. Note that $EBROOTTRIMMOMATIC is only available if the Trimmomatic module has been loaded.
Note that the adapter
sequence files are
in /opt/software-current/2023.06/x86_64/generic/software/Trimmomatic/0.39-Java-17/adapters/ (or if the module has been loaded, $EBROOTTRIMMOMATIC/adapters). If you
couldn't find the adapters you need in that directory, you will need to
obtain them from elsewhere (for example asking the person who ran the
library prep for you).