recipe scramble

Soft Clipped Read Alignment Mapper

Homepage

https://github.com/GeneDx/scramble

License

CC

Recipe

/scramble/meta.yaml

Links

doi: 10.1038/s41436-020-0749-x

SCRAMble identifies clusters of soft clipped reads in a BAM file, builds consensus sequences, aligns to representative L1Ta, AluYa5, and SVA-E sequences, and outputs MEI calls

package scramble

(downloads) docker_scramble

Versions

1.0.1-11.0.1-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install scramble

and update with:

conda update scramble

or use the docker container:

docker pull quay.io/biocontainers/scramble:<tag>

(see scramble/tags for valid values for <tag>)

Notes

SCRAMble runs as a two-step process. First cluster_identifier is used to generate soft-clipped read cluster consensus sequences. Second, SCRAMble.R analyzes the cluster file for likely MEIs. Custom wrapper script scramble.sh is provided to help setting location of SCRAMble.R script, and values for --install-dir and --mei-refs params.

Download stats