sortgff

sortgff sorts General Feature Format (GFF) files to order genomic feature records by genomic coordinates or other specified criteria for downstream genomic analyses.

Key Features:

• Integration with Galaxy@Pasteur: Integrated into the Galaxy@Pasteur instance to execute within Galaxy's execution engine.
• GFF sorting: Produces consistently ordered GFF outputs by sorting feature entries according to genomic coordinates or user-specified criteria.
• Scalability: Operates within a scalable Galaxy computational environment to process large GFF datasets.
• API and library support: Communicates with the Galaxy platform via the Galaxy API or the Bioblend library for job submission and management.

Scientific Applications:

• Genome annotation: Provides ordered GFF input required by genome annotation pipelines.
• Comparative genomics: Enables consistent ordering of genomic features to facilitate comparisons across species or strains.
• Functional genomics: Supplies organized feature files to support analyses of gene function and regulation.

Methodology:

Runs inside the Galaxy framework using its execution engine; it reads an unsorted GFF file, organizes entries based on genomic coordinates or other specified criteria, outputs a sorted GFF file, and interacts with Galaxy via the Galaxy API or Bioblend.