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.

¹Version-specific preformatted PhyloDB, EukProt, and MMETSP databases are available at the following path: /data/reference/eukulele/

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_DB - database directory

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