gff3sort

gff3sort sorts GFF3 files to produce results suitable for tabix indexing and JBrowse rendering.

Key Features:

• Parent-child topology sorting: Conducts parent-child topology sorting for features with the same chromosome and start position.
• Original order retention: Remembers original orders of features that share the same chromosome and start position.
• JBrowse compatibility: Produces sorting results specifically designed for accurate rendering in JBrowse.
• Cross-species validation: Tested on datasets from seven species with accurate sorting results and acceptable efficiency.

Scientific Applications:

• Genome annotation visualization: Enables visualization of gene annotation data in JBrowse via tabix-indexed sorted GFF3 files rather than JSON conversion.
• Genome annotation data processing: Facilitates processing of GFF3 format genome annotation files for downstream analysis and visualization workflows.

Methodology:

gff3sort is implemented as a Perl script that sorts GFF3 files by chromosome and start position, with special handling for features sharing the same coordinates through either original order retention or parent-child topology sorting.