This repository is a collection of modules written in bash that are used to run the simulated longread fusion transcript detector.

The src directory contains files relevant to the pipeline. The pipeline is meant to be run in the asscociated docker image located at https://hub.docker.com/repository/docker/vantwisk/longread-fusion-transcript-pipeline/general.

The pipeline will produce the ref, sim, alignments, and results directories in the bound folder. The results directory contains the fusion results for the various tools as well as the output graphs in the graphs directory.

Files in the ref directory can be used for subsequent runs. Otherwise, the pipeline will populate it with needed resources to run the pipeline.