EUKulele¶
Description¶
EUKulele is a Python program for taxonomic annotation of microbes in metatranscriptomic and metagenomic samples, with special emphasis on eukaryote discovery. The software includes four major features: * Database setup and formatting * Database creation, alignment, and taxonomic estimation * Assessment of the BUSCO completeness of subsets of contigs at each taxonomic level * Assessment of taxonomic classification using only BUSCO-identified core eukaryotic genes In principle, there are two prerequisites for running the software: 1. Metagenomic or metatranscriptomic sample files (unless using the provided sample data) 2. A database to which to align the contigs from the metagenome or metatranscriptome. EUKZoo databases are available at the following path: /data/reference/eukulele/2.0.7
Environment Modules¶
Run module spider eukulele to find out what environment modules are available for this application.
Environment Variables¶
- HPC_EUKULELE_DIR - installation directory
- HPC_EUKULELE_BIN - executable directory
- HPC_EUKULELE_PHYLODB_DB - PhyloDB database directory
- HPC_EUKULELE_EUKPROT_DB - EukProt database directory
- HPC_EUKULELE_MMETSP_DB - MMETSP database directory
- HPC_EUKULELE_EUKZOO_DB - EukZoo database directory
Categories¶
alignment, biology, genomics