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:

Metagenomic or metatranscriptomic sample files (unless using the provided sample data)
A database¹ to which to align the contigs from the metagenome or metatranscriptome.

¹As a courtesy, HiPerGator hosts version-specific preformatted EukProt, EUKZOO, MMETSP, and PhyloDB databases at the following path: /data/reference/eukulele/. If you do not specify your database path, it will be downloaded unnecessarily to your working directory. Follow usage example below.

Environment Modules

Run module spider eukulele to find out what environment modules are available for this application.

System Variables

HPC_EUKULELE_DIR - installation directory
HPC_EUKULELE_BIN - executable directory
HPC_EUKULELE_EUKPROT_DB - EukProt database directory
HPC_EUKULELE_EUKZOO_DB - EukZoo database directory
HPC_EUKULELE_MMETSP_DB - MMETSP database directory
HPC_EUKULELE_PHYLODB_DB - PhyloDB database directory

Additional Information

Usage: $ EUKulele --help

Example command:

$ EUKulele all --m mets --sample_dir ./metatranscriptomes/ --database phylodb --reference_dir ${HPC_EUKULELE_PHYLODB_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