JOA: Joint Overlap Analysis of multiple genomic interval sets.

ABSTRACT:

Background

Next-generation sequencing (NGS) technologies have produced large volumes of genomic data. One common operation on heterogeneous genomic data is genomic interval intersection. Most of the existing tools impose restrictions such as not allowing nested intervals or requiring intervals to be sorted when finding overlaps in two or more interval sets.

Results

We proposed segment tree (ST) and indexed segment tree forest (ISTF) based solutions for intersection of multiple genomic interval sets in parallel. We developed these methods as a tool, Joint Overlap Analysis (JOA), which takes n interval sets and finds overlapping intervals with no constraints on the given intervals. The proposed indexed segment tree forest is a novel composite data structure, which leverages on

SUBMITTER: Otlu B 

PROVIDER: S-EPMC6408804 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature