funannotate2¶
Description¶
Funannotate2 is a comprehensive eukaryotic genome annotation pipeline that provides a complete workflow for annotating fungal, plant, and other eukaryotic genomes. It integrates various tools and databases to produce high-quality gene predictions and functional annotations.
Key features: * Genome cleaning and preparation * Gene prediction using multiple methods (Augustus, GeneMark-ES, SNAP, GlimmerHMM, etc.) * Automated ab-initio training of gene prediction algorithms * Evidence-based gene prediction using transcript and protein alignment evidence * Functional annotation using various databases (Pfam, dbCAN, MEROPS, SwissProt, etc.) * BUSCO-based quality assessment * Output in various formats (GFF3, GenBank, FASTA, etc.)
Environment Modules¶
Run module spider funannotate2 to find out what environment modules are available for this application.
Environment Variables¶
- HPC_FUNANNOTATE2_DIR - installation directory
- HPC_FUNANNOTATE2_BIN - executable directory
- FUNANNOTATE2_DB - funannotate database directory
- GENEMARK_PATH - genmark directory
Categories¶
biology, genomics, annotation