Abstract
Motivation 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 bugs that would lead to erroneous rendering in JBrowse.
Results We developed GFF3sort, a script to sort GFF3 files for tabix indexing. GFF3sort can properly deal with the order of features that have the same chromosome and start position. Based on our test datasets from multiple species, GFF3sort produced accurate sorting results while taking significantly less running time compared with currently available tools. We anticipate that GFF3sort will be a useful tool to help with genome annotation data processing and visualization.
Availability https://github.com/billzt/gff3sort
