pegi3s/fastqc 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 FastQC⁠, a quality control tool for high throughput sequence data.

⁠Using the FastQC image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/fastqc /data/input.fq

In this command, you should replace:

• /your/data/dir to point to the directory that contains the FASTQ file you want to analyze.
• input.fq to the actual name of your input file.

To see the FastQC help, just run docker run --rm pegi3s/fastqc --help.

⁠Running the FastQC GUI in Linux

This docker image can be also used to run the FastQC GUI. To do so, just run: docker run --rm -ti -e USERID=$UID -e USER=$USER -e DISPLAY=$DISPLAY -v /var/db:/var/db:Z -v /tmp/.X11-unix:/tmp/.X11-unix -v $HOME/.Xauthority:/home/developer/.Xauthority -v "/your/data/dir:/data" pegi3s/fastqc

If the above command fails, try running xhost + first.

Note that FastQC can deal with both compressed and uncompressed FASTQ files. You can also speed up the execution by adding -t 4 to tell FastQC to use 4 cores (it uses 1 core by default).