Usage

Tip

Version-specific preformatted PhyloDB, EukProt, MMETSP, and EUKZoo databases are available using the environment variables above.

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.

Run the following to get a list of helpful commands and tips inside the EUKulele module: 

$ EUKulele --help
Example command: 
$ EUKulele --sample_dir ./metatranscriptomes/ -m mets --database mmetsp --reference_dir ${HPC_EUKULELE_MMETSP_DB} --CPUs ${SLURM_CPUS_PER_TASK}