This component runs Trimmomatic on paired-end FastQ files but uses information on the per-base GC content variation reported by FastQC to guide the trimming of the FastQ reads.
Software pages: FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/); Trimmoatic (http://www.usadellab.org/cms/?page=trimmomatic)
- Input type:
- Output type:
The default input parameter for FastQ data is
--fastq. You can change
--fastq parameter default pattern (
to input file names (e.g.:
adapters: Provide a non-default fasta file containing the adapter sequences used to screen overrepresented sequences against and to filter the FastQ files.
trimSlidingWindow: Perform sliding window trimming, cutting once the average quality within the window falls below a threshold.
trimLeading: Cut bases off the start of a read, if below a threshold quality.
trimTrailing: Cut bases of the end of a read, if below a threshold quality.
trimMinLength: Drop the read if it is below a specified length.
results/trimmomatic: The trimmed FastQ files for each sample.
reports/fastqc: Stores the FastQC HTML reports for each sample and a
FastQC_trim_report.csvfile containing the trimming values suggested by the analysis of the FastQC report.
reports/fastqc/run_1/: Stores the summary text files with the category results of FastQC for each sample.
memory: 4GB (dynamically increased on retry)