JOA: Joint Overlap Analysis of multiple genomic interval sets.

We implemented JOA in Java using the fork/join framework which speeds up parallel processing by taking advantage of all available processor cores. We compared JOA ST with JOA ISTF and showed that segment tree and indexed segment tree forest methods are comparable with each other in terms of execution time and memory usage. We also carried out execution time comparison analysis for JOA and other tools and demonstrated that JOA has comparable execution time and is able to further reduce its running time by using more processors per node. JOA can be run using its GUI or as a command line tool. JOA is available with source code at https://github.com/burcakotlu/JOA/ . A user manual is provided at https://joa.readthedocs.org.