pegi3s/seqkit 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 the SeqKit⁠ suite - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. Frequently used tools in this suite are⁠:

• Sequence and subsequence:

  • seq
  • subseq
  • sliding
  • stats
  • faidx
  • watch
  • sana

• Format conversion:

  • fq2fa
  • fx2tab & tab2fx
  • convert
  • translate

• Searching:

  • grep
  • locate
  • fish
  • amplicon

• BAM processing and monitoring

  • bam

• Set Operations:

  • head
  • range
  • sample
  • rmdup
  • duplicate
  • common
  • split
  • split2

• Edit:

  • replace
  • rename
  • restart
  • concat
  • mutate

• Ordering:

  • shuffle
  • sort

• Misc:

  • genautocomplete

To obtain the help of an application, you just need to run: docker run --rm pegi3s/seqkit <seqkit-application-name> --help (e.g. docker run --rm pegi3s/seqkit subseq --help)

⁠Using the SeqKit image in Linux

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

In this command, you should replace:

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

⁠Using the SeqKit 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/seqkit <seqkit-application-name> <options>