pegi3s/trimmomatic repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of Trimmomatic⁠, a fastq trim and filter tool.

⁠Using the Trimmomatic image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/trimmomatic <SE or PE> <phred> /data/input.fastq /data/output.fastq

In this command, you should replace:

• /your/data/dir to point to the directory that contains the FASTQ file you want to process.
• input.fastq to the actual name of your input file.
• <SE or PE> to SE in case of single-end sequencing and PE in case of paired-end sequencing.
• <phred> to either -phred33 or -phred64
• output.fastq to the actual name of your output fastq file.

To see the trimmomatic usage, just run docker run --rm pegi3s/trimmomatic PE (or SE). To see the version, run docker run --rm pegi3s/trimmomatic -version.