GOMAP

GOMAP annotates plant genomes with Gene Ontology (GO) terms at genome scale to provide reproducible functional annotations for biological inference.

Key Features:

• High-throughput, reproducible pipeline: An optimized pipeline for genome-scale GO term assignments that enables reproducible annotation across computational environments.
• Singularity containerization: Packaged as a Singularity container to enable deployment in high-performance computing (HPC) environments.
• HPC performance optimization: Workflow and resource optimizations for efficient processing of large, repetitive plant genomes on HPC systems.
• Comprehensive functional annotation: Expands the number of genes annotated and annotations per gene and improves GO assignment quality, including improved Fmax in maize test cases.

Scientific Applications:

• Plant species annotation: Applied to maize, wheat, rice, barley, cotton, and soy to generate high-coverage, reproducible GO annotation sets.
• Genomic research: Facilitates functional interpretation of genes within complex plant genomes.
• Comparative genomics: Enables standardized functional annotations for cross-species comparisons.
• Breeding and genetic engineering: Supports identification of candidate genes for breeding programs and genetic modification.

Methodology:

GOMAP assigns Gene Ontology terms using an optimized, reproducible pipeline containerized with Singularity and configured for high-performance computing, demonstrated on maize.