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.

Upload more screenshots

Please help extend the collection of screenshots. Just make a screenshot and upload it here. You don't need to register or anything.

Upload a screenshot

Hint: upload an image here from your clipboard with Ctrl-V


Install this software package

If the package is available for the distribution you are currently using on your computer then install the software by clicking on…

Install trimmomatic