sentieon/sentieon-cli repository overview

⁠Quick Reference:

⁠Sentieon-cli

The source code for the sentieon-cli can be found at, https://github.com/Sentieon/sentieon-cli⁠

⁠Sentieon documentation

Find documentation for the sentieon-cli at https://support.sentieon.com/docs/sentieon_cli/⁠.

⁠Where to get help:

If you encounter issues or have any question, please contact Sentieon support at [email protected]⁠.

⁠What is Sentieon?

Sentieon provides complete solutions for secondary DNA analysis. Our software improves upon BWA, GATK, Mutect, and Mutect2 based pipelines. The Sentieon tools are deployable on any generic-CPU-based computing system.

⁠About the Sentieon tools

The Sentieon tools are enterprise-strength software tools that are inherently multi-threading and distributed-processing ready; the Sentieon tools do not downsample in high coverage regions and have zero run-to-run difference. The Sentieon tools are an easily deployable software only solution for your DNA sequencing data analysis needs.

⁠How to use this image?

This image contains the Sentieon software and the sentieon-cli⁠. Please refer to the sentieon-cli documentation for usage information.

⁠Obtaining a license

Email [email protected]⁠ or visit https://www.sentieon.com/free-trial/⁠ to request a license.

⁠Usage example

docker pull sentieon/sentieon_cli:v1.6.1-0
docker run --rm -v "$PWD:/data" -w /data \
    sentieon/sentieon_cli:v1.6.1-0 \
    sentieon-cli dnascope-pangenome --help

⁠Bioinformatics tools included in the latest container image

⁠A note on the multiqc installation

The python environment included in this container image does not include the kaleido or pyarrow packages, which are used by multiqc to generate output in non-default file formats.

⁠License:

The Sentieon tools are commercial software and a license is required for their download and use. By using this container image you agree to the terms of the Sentieon End User License Agreement, https://www.sentieon.com/EULA/eula-aws.html⁠.

In addition to the Sentieon software, these images also contain software which may be under other licenses (Bash, etc.). As for any pre-built image usage, it is the image user's responsibility to ensure that any use of this image complies with any relevant licenses for all software contained within.