pegi3s/seqkit

Sponsored OSS

By i3S

Updated 4 months ago

SeqKit (https://github.com/shenwei356/seqkit/blob/master/README.md) docker image.

Image
Data Science
Languages & Frameworks

3.4K

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/.

Docker Pull Command

docker pull pegi3s/seqkit