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EUKulele

Description

eukulele website

EUKulele is a Python program for taxonomic annotation of microbes in metatranscriptomic and metagenomic samples, with special emphasis on eukaryote discovery.

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

Additional Usage Information

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}

Citation

If you publish research that uses eukulele you have to cite it as follows:

  • Krinos AI, Hu SK, Cohen NR, Alexander H. EUKulele: taxonomic annotation of the unsung eukaryotic microbes. J Open Source Softw. 2021;6(57):2817. https://doi.org/10.21105/joss.02817

Categories

alignment, biology, genomics