chrishah/trimmomatic-docker repository overview

⁠trimmomatic-docker

Docker image for trimmomatic

The image contains a full install of trimmomatic⁠, including all necessary dependencies. I am not part of the trimmomatic team - I just made this image.

In detail, the image is set up with:

• Ubuntu 16.04
• openjdk version "1.8.0_191"
• trimmomatic 0.38

To run trimmomatic⁠ you can do the following (this will mount the directory /home/working of the container to the current working directory on your local machine):

$ docker run -it --rm -v $(pwd):/home/working -w /home/working chrishah/trimmomatic:0.38 trimmomatic

If you want to use the ILLUMINACLIP option of Trimmomatic, the adapterfiles that ship with Trimmomatic are also in the container, in the location: /usr/src/Trimmomatic/0.38/Trimmomatic-0.38/adapters/. So if you want to use one of those, say TruSeq3-PE-2.fa, you can make a variable with the full path to this file in the container (see below). Note that via the docker container you can only access files that are in, or below, your mountpoint (the directory you specify with -v). An example for an actual trimmomatic usage with adapter trimming is here:

prefix=sample
forw=./rawreads/reads.1.fastq.gz
reve=./rawreads/reads.2.fastq.gz
threads=6
adapterfile=/usr/src/Trimmomatic/0.38/Trimmomatic-0.38/adapters/TruSeq3-PE-2.fa

docker run -it --rm -v $(pwd):/home/working -w /home/working chrishah/trimmomatic:0.38 trimmomatic PE \
-threads $threads -phred33 $forw $reve \
$prefix\_forward.paired.fastq.gz $prefix\_forward.singletons.fastq.gz \
$prefix\_reverse.paired.fastq.gz $prefix\_reverse.singletons.fastq.gz \
ILLUMINACLIP:$adapterfile:2:30:10 TRAILING:30 LEADING:30 SLIDINGWINDOW:5:20 MINLEN:100 &> $prefix.trim.log