GFF3sort: a novel tool to sort GFF3 files for tabix indexing.

ABSTRACT:

Background

The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexed by tabix, a novel strategy that is more convenient than the original conversion process. However, current tools available for GFF3 file sorting have some limitations and their sorting results would lead to erroneous rendering in JBrowse.

Results

We developed GFF3sort, a script to sort GFF3 files for tabix indexing. Specifically designed for JBrowse rendering, GFF3sort can properly deal with the order of features that have the same chromosome and start position, either by remembering their original orders or by conducting parent-child topology sorting. Based

SUBMITTER: Zhu T 

PROVIDER: S-EPMC5686826 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature