TrimGalore! is a “wrapper script” written to automate adaptor trimming and quality control. This program will detect adapters present, and remove very low quality reads (quality score <20) by default. For more information, or to download, visit TrimGalore!.

Note: Many assemblers do not recommend trimming and thinning data, but it beneficial for downstream analyses. Consider what type of data you are processing. For example, PacBio data is error-corrected by the assembler, but it is common to procceed with trimming and thinning of Illumina data.

To run TrimGalore on your genomic data, be sure that the TrimGalore! module is available and loaded on your HPC, and write a job script using the following code:

 echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
#
#trimgalore command, call paired fastq files
trim_galore --paired --retain_unpaired <file_1.fastq> <file_2.fastq>
#
 echo = `date` job $JOB_NAME done

Once the job is complete, you can run FastQC again to assess changes in the files.