bioinfoipec/afterqc repository overview

⁠AfterQC

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

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data bioinfoipec/afterqc afterqc.py -1 /data/input_R1.fq -2 /data/input_R2.fq -g /data/output -b /data/output -r /data/output

This command will save the output files in output directory. With the good reads, bad reads and the report containing 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 bioinfoipec/afterqc afterqc.py --help.

Note that the fastq file does not need to be descompressed as AfterQC can deal with both compressed and uncompressed FASTQ files.

⁠Test data

To test the previous command, you can use the files in testdata directory and type as following:

docker run --rm -v /dockerfiles/testdata/:/data bioinfoipec/afterqc afterqc.py -1 /data/R1.fq -1 /data/R2.fq -g /data/output -b /data/output -r /data/output