Telomerecat is a tool for estimating the average telomere length (TL) for a paired end, whole genome sequencing (WGS) sample.
Telomerecat is adaptable, accurate and fast. The algorithm accounts for sequencing amplification artifacts, anneouploidy (common in cancer samples) and noise generated by WGS. For a high coverage WGS BAM file of around 100GB telomerecat can produce an estimate in ~1 hour.
Telomerecat is available as a Docker container on Quay.io.
No "latest" image is defined, you need to specify the version you require, e.g.:
export VERSION_TEL=3.4.1 # update as appropriate
docker pull quay.io/wtsicgp/telomerecat:${VERSION_TEL}
The docker container is known to work with singularity, save the image locally via:
export VERSION_TEL=3.4.1 # update as appropriate
singularity pull docker://quay.io/wtsicgp/telomerecat:${VERSION_TEL}
Installation is via pip
. Simply execute with the URL to a package release, e.g.:
pip3 install telomerecat
Please see the command line help:
telomerecat --help
When selecting the number of processes/threads the following should be considered:
pip
will install the relevant dependancies, listed here for convenience:
You will need virtualenv available on your system.
cd $PROJECTROOT
python3 -m venv env
source env/bin/activate
python setup.py develop # so bin scripts can find module
setup.py
has been updatedsetup.py
/Dockerfile
CircleCI will handle docker image push to quay.io and package deployment to pypi.