pegi3s/afterqc 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 AfterQC⁠, a program for automatic filtering, trimming, error removing and quality control of FASTQ files.

⁠Using the AfterQC image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/afterqc bash -c "cd /data && after.py -1 /data/input.fq"

This command generates three folders automatically, a folder good stores the good reads, a folder bad stores the bad reads and a folder QC stores the report of quality control.

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 AfterQC help, just run docker run --rm pegi3s/afterqc after.py -h.