abruyneel/alleleprofiler repository overview

Gene editing strategies, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9), are revolutionizing biochemistry. Potent, yet flexible, bioinformatics technologies are required to aid in the profiling of the generated transgenic cell lines, plants or animals. Here, we present AlleleProfileR, a novel analysis tool, written in a combination of R and C++, with the ability to batch process the sequence analysis of large and complex experiments, including base editing and large deletions created by using two guides.

The full source of AlleleProfileR can be found on GitHub (https://github.com/abruyneel/AlleleProfileR⁠). This docker provides a minimal working environment for using AlleleProfileR. It incorporates several external tools such as samtools and bwa such that processed sequencing files can be analyzed. The Dockerfile found be found at https://github.com/abruyneel/AlleleProfileR_docker⁠.

To run:

docker run --rm -e PASSWORD=crispr -p 8787:8787 abruyneel/alleleprofiler

Version History

v1.3: 06/03/2020, updated R version (R 4.0.0)

v1.2: 11/02/2019, version of at the time of the publication (R 3.6.1)