GeneForge

GeneForge orchestrates the parallel execution of BRAKER3 and FunAnnotate for comprehensive structural and functional annotation of eukaryotic genomes, evaluates their performance using BUSCO, and provides a unified functional annotation suite.

Key Features:

• Parallel Gene Prediction: Executes BRAKER3 and FunAnnotate simultaneously for eukaryotic genome annotation.
• Annotation Evaluation: Uses BUSCO to evaluate and compare the performance of multiple annotation pipelines.
• Backbone-Complement Merging: Implements COMPARE_BUSCO to evaluate and select a primary backbone annotation, then complements it with missing models via MERGE_ANNOTATIONS.
• tRNA Integration: Automates tRNA merging into consensus annotation results.
• Overlap Resolution: Integrates AGAT for overlap resolution and coordinate finalization.

Scientific Applications:

• Eukaryotic Genome Annotation: Generates structural and functional annotations for eukaryotic genomes through integrated pipeline execution.
• Annotation Quality Assessment: Evaluates and selects optimal gene models using BUSCO-based benchmarking metrics.
• Consensus Annotation Construction: Merges complementary gene predictions to produce a unified, non-redundant annotation set.

Methodology:

GeneForge is implemented as a Nextflow pipeline that orchestrates parallel execution of BRAKER3 and FunAnnotate, evaluates outputs with BUSCO, selects a primary backbone via COMPARE_BUSCO, complements it with missing models through MERGE_ANNOTATIONS, automates tRNA merging, and uses AGAT for overlap resolution and coordinate finalization.