Trimmomatic
Trimmomatic is capable of performing a variety of trimming tasks for illumina generated paired-end and single end data. If no thread count is provided it is determined automatically. The available commands include:
| Command | Description |
|---|---|
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 its below a specified length |
tophred33 | convert quality scores to phred-33 |
tophred64 | convert quality scores to phred-66 |
For additional information please see the documentation
ml biocontainers trimmomatic
trimmomatic -threads 20 -phred33 -trimlog log.txt input.fa output.fa
Parallel Capabilities: Some commands have Multithreading options supported. Please see documentation.