pegi3s/seqtk 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 allows the usage of seqtk⁠, a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.

To show the available commands, just run: docker run --rm pegi3s/seqtk.

To obtain the help of a command, you just need to run: docker run --rm pegi3s/seqtk <seqtk-command> (e.g. docker run --rm pegi3s/seqtk split)

⁠Using the seqtk image in Linux

To run an application, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/seqtk <seqtk-command> <options>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <seqtk-command> to the name of the seqtk application you want to use.
• <options> with the specific options of the seqtk command. These options will include the input/output files, which should be referenced under /data/.

⁠Using the seqtk image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

As in the Linux case, to run an application, you should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/seqtk <seqtk-command> <options>