pegi3s/paf2chain 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 paf2chain⁠, a tool for alignment format conversion.

⁠Using the paf2chain image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/paf2chain bash -c "paf2chain -i /data/pafFile > /data/output.chain"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input file(s).
• pafFile to the actual name of your PAF file. It must contain CIGAR strings in the cg:Z: tag.
• output.chain to the actual name of your output file.

To see the paf2chain⁠ help, just run docker run --rm pegi3s/paf2chain --help.