TrimmomaticSE

flexible read trimming tool for Illumina NGS data

Install

All systems
curl cmd.cat/TrimmomaticSE.sh
Debian Debian
apt-get install trimmomatic
Ubuntu
apt-get install trimmomatic
image/svg+xml Kali Linux
apt-get install trimmomatic
Windows (WSL2)
sudo apt-get update sudo apt-get install trimmomatic
Raspbian
apt-get install trimmomatic

trimmomatic

flexible read trimming tool for Illumina NGS data

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 thes 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 * MINLENGTH: 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.