EukMetaSanity

EukMetaSanity performs gene prediction and annotation for eukaryotic genomes, enabling large-scale processing of metagenome-assembled genomes (MAGs) and reference genomes for downstream genomic analysis.

Key Features:

• Automated Taxonomy Search: Searches a comprehensive protein database of 1,482 species to identify phylogenetically compatible proteins for downstream prediction.
• Three-Pipeline Design: Implements three distinct pipelines optimized for extensive parallelization on high-performance computing infrastructures.
• Gene Prediction Capabilities: Predicts introns, exons, and gene loci across diverse eukaryotic genomes.
• Empirical Testing: Has been tested on 112 genomes spanning fungi, plants, and animals, and on 1,669 MAGs sourced from NCBI.
• Scalability: Produces preliminary gene predictions for individual target taxa and at large scale across hundreds of MAGs.

Scientific Applications:

• Environmental Metagenomics: Enables gene prediction and annotation for MAGs recovered from environmental samples.
• Targeted Taxonomic Studies: Generates preliminary gene models for focused analyses of specific eukaryotic taxa.
• Broad-Scale Genomic Surveys: Supports high-throughput annotation across hundreds to thousands of genomes or MAGs.
• Eukaryotic Biodiversity and Evolution: Facilitates genome annotation to inform studies of biodiversity and evolutionary relationships.

Methodology:

Performs an automated taxonomy search against a 1,482-species protein database to identify phylogenetically compatible proteins; executes three pipelines optimized for parallelization on high-performance computing infrastructures; and conducts intron, exon, and gene locus prediction.