pegi3s/seqkit
SeqKit (https://github.com/shenwei356/seqkit/blob/master/README.md) docker image.
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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:
Format conversion:
Searching:
BAM processing and monitoring
Set Operations:
Edit:
Ordering:
Misc:
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
)
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 pegi3s/seqkit