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.

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 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/. See usage 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

Specify pre-installed database: e.g.,

$ EUKulele [subroutine] --reference_dir ${HPC_EUKULELE_PHYLODB_DB}

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